diff --git a/src/mito2/src/compaction.rs b/src/mito2/src/compaction.rs
index 8a52ed2398..5c558df4f5 100644
--- a/src/mito2/src/compaction.rs
+++ b/src/mito2/src/compaction.rs
@@ -278,15 +278,23 @@ impl CompactionScheduler {
                 }
                 options @ Options::StrictWindow(_) => {
                     // Incoming compaction request is manually triggered.
-                    status.set_pending_request(PendingCompaction {
-                        options,
-                        waiter,
-                        max_parallelism,
-                    });
-                    info!(
-                        "Region {} is compacting, manually compaction will be re-scheduled.",
-                        region_id
-                    );
+                    if status.pending_ddl_requests.is_empty() {
+                        status.set_pending_request(PendingCompaction {
+                            options,
+                            waiter,
+                            max_parallelism,
+                        });
+                        info!(
+                            "Region {} is compacting, manually compaction will be re-scheduled.",
+                            region_id
+                        );
+                    } else {
+                        waiter.send(CompactionCancelledSnafu.fail());
+                        info!(
+                            "Region {} has pending DDL requests, cancelling manual compaction.",
+                            region_id
+                        );
+                    }
                 }
             }
             return Ok(false);
@@ -4676,6 +4684,88 @@ mod tests {
         assert!(scheduler.has_pending_ddls(region_id));
     }
 
+    #[tokio::test]
+    async fn test_pending_ddl_rejects_later_manual_compaction() {
+        let env = SchedulerEnv::new().await;
+        let (tx, _rx) = mpsc::channel(4);
+        let mut scheduler = env.mock_compaction_scheduler(tx);
+        let builder = VersionControlBuilder::new();
+        let version_control = Arc::new(builder.build());
+        let region_id = builder.region_id();
+        let manifest_ctx = env
+            .mock_manifest_context(version_control.current().version.metadata.clone())
+            .await;
+        let (schema_metadata_manager, _kv_backend) = mock_schema_metadata_manager();
+
+        let mut status =
+            CompactionStatus::new(region_id, version_control.clone(), env.access_layer.clone());
+        status.start_local_task();
+        scheduler.region_status.insert(region_id, status);
+
+        let (first_manual_tx, mut first_manual_rx) = oneshot::channel();
+        assert!(
+            !scheduler
+                .schedule_compaction(
+                    region_id,
+                    compact_request::Options::StrictWindow(StrictWindow { window_seconds: 60 }),
+                    &version_control,
+                    &env.access_layer,
+                    OptionOutputTx::from(first_manual_tx),
+                    &manifest_ctx,
+                    schema_metadata_manager.clone(),
+                    1,
+                )
+                .unwrap()
+        );
+
+        let (ddl_tx, _ddl_rx) = oneshot::channel();
+        scheduler.add_ddl_request_to_pending(SenderDdlRequest {
+            region_id,
+            sender: OptionOutputTx::from(ddl_tx),
+            request: crate::request::DdlRequest::EnterStaging(
+                store_api::region_request::EnterStagingRequest {
+                    partition_directive:
+                        store_api::region_request::StagingPartitionDirective::RejectAllWrites,
+                },
+            ),
+        });
+
+        let (later_manual_tx, mut later_manual_rx) = oneshot::channel();
+        assert!(
+            !scheduler
+                .schedule_compaction(
+                    region_id,
+                    compact_request::Options::StrictWindow(StrictWindow {
+                        window_seconds: 120,
+                    }),
+                    &version_control,
+                    &env.access_layer,
+                    OptionOutputTx::from(later_manual_tx),
+                    &manifest_ctx,
+                    schema_metadata_manager,
+                    1,
+                )
+                .unwrap()
+        );
+
+        let later_result = later_manual_rx
+            .try_recv()
+            .expect("manual compaction queued after DDL was not rejected");
+        assert_matches!(later_result.unwrap_err(), Error::CompactionCancelled { .. });
+        assert_matches!(
+            first_manual_rx.try_recv(),
+            Err(oneshot::error::TryRecvError::Empty)
+        );
+        let pending_request = scheduler.region_status[&region_id]
+            .pending_request
+            .as_ref()
+            .expect("manual compaction queued before DDL was removed");
+        assert_matches!(
+            &pending_request.options,
+            compact_request::Options::StrictWindow(StrictWindow { window_seconds: 60 })
+        );
+    }
+
     #[tokio::test]
     async fn test_request_cancel_state_transitions() {
         let env = SchedulerEnv::new().await;
diff --git a/src/mito2/src/engine/compaction_test.rs b/src/mito2/src/engine/compaction_test.rs
index d5cbc94aec..8e5064226c 100644
--- a/src/mito2/src/engine/compaction_test.rs
+++ b/src/mito2/src/engine/compaction_test.rs
@@ -22,14 +22,15 @@ use api::v1::{ColumnSchema, Rows};
 use common_error::ext::ErrorExt;
 use common_error::status_code::StatusCode;
 use common_recordbatch::{RecordBatches, SendableRecordBatchStream};
+use common_time::Timestamp;
 use datatypes::arrow::array::AsArray;
 use datatypes::arrow::datatypes::TimestampMillisecondType;
 use store_api::region_engine::{RegionEngine, RegionRole};
 use store_api::region_request::AlterKind::SetRegionOptions;
 use store_api::region_request::{
     EnterStagingRequest, PathType, RegionAlterRequest, RegionCloseRequest, RegionCompactRequest,
-    RegionDeleteRequest, RegionFlushRequest, RegionOpenRequest, RegionRequest, SetRegionOption,
-    StagingPartitionDirective,
+    RegionDeleteRequest, RegionFlushRequest, RegionOpenRequest, RegionRequest,
+    RegionTruncateRequest, SetRegionOption, StagingPartitionDirective,
 };
 use store_api::storage::{RegionId, ScanRequest};
 use tokio::sync::Notify;
@@ -453,7 +454,6 @@ async fn test_pending_manual_compaction_finishes_before_queued_ddl() {
         .unwrap();
     put_and_flush(&engine, region_id, &column_schemas, 0..10).await;
     put_and_flush(&engine, region_id, &column_schemas, 5..20).await;
-
     let commit_guard = gate.arm_commit();
     let regular_engine = engine.clone();
     let regular_task = tokio::spawn(async move {
@@ -717,6 +717,284 @@ async fn test_enter_staging_waits_for_picking_logical_cancellation_ack() {
     assert!(engine.get_region(region_id).unwrap().is_staging());
 }
 
+#[tokio::test]
+async fn test_truncate_waits_for_cancellable_compaction() {
+    common_telemetry::init_default_ut_logging();
+    let mut env = TestEnv::new().await;
+    let region_id = RegionId::new(9, 1);
+    let gate = Arc::new(CompactionPlanningGate::new(region_id));
+    let engine = env
+        .create_engine_with(
+            MitoConfig {
+                num_workers: 1,
+                min_compaction_interval: Duration::from_secs(60 * 60),
+                ..Default::default()
+            },
+            None,
+            Some(gate.clone()),
+            None,
+        )
+        .await;
+    env.get_schema_metadata_manager()
+        .register_region_table_info(
+            region_id.table_id(),
+            "truncate_during_cancellable_compaction",
+            "test_catalog",
+            "test_schema",
+            None,
+            env.get_kv_backend(),
+        )
+        .await;
+    let create = CreateRequestBuilder::new()
+        .insert_option("compaction.type", "twcs")
+        .build();
+    let column_schemas = create
+        .column_metadatas
+        .iter()
+        .map(column_metadata_to_column_schema)
+        .collect::<Vec<_>>();
+    engine
+        .handle_request(region_id, RegionRequest::Create(create))
+        .await
+        .unwrap();
+    put_and_flush(&engine, region_id, &column_schemas, 0..10).await;
+    put_and_flush(&engine, region_id, &column_schemas, 5..20).await;
+
+    let planning_guard = gate.arm();
+    let compact_engine = engine.clone();
+    let compact_task = tokio::spawn(async move {
+        compact_engine
+            .handle_request(
+                region_id,
+                RegionRequest::Compact(RegionCompactRequest::default()),
+            )
+            .await
+    });
+    tokio::time::timeout(Duration::from_secs(5), gate.wait_until_entered())
+        .await
+        .expect("compaction did not reach the cancellable planning gate");
+
+    let truncate_engine = engine.clone();
+    let mut truncate_task = tokio::spawn(async move {
+        truncate_engine
+            .handle_request(
+                region_id,
+                RegionRequest::Truncate(RegionTruncateRequest::All),
+            )
+            .await
+    });
+    tokio::time::timeout(Duration::from_secs(5), async {
+        tokio::select! {
+            biased;
+            result = &mut truncate_task => {
+                panic!("truncate completed before cancellable compaction terminated: {result:?}");
+            }
+            () = gate.wait_until_cancel_requested() => {}
+        }
+    })
+    .await
+    .expect("truncate did not request compaction cancellation");
+    assert!(!truncate_task.is_finished());
+
+    let pending_ddl_guard = gate.arm_pending_ddl_dispatch();
+    planning_guard.release();
+    tokio::time::timeout(
+        Duration::from_secs(5),
+        gate.wait_until_pending_ddl_dispatch(),
+    )
+    .await
+    .expect("cancelled compaction did not reach pending truncate dispatch");
+    let compact_err = tokio::time::timeout(Duration::from_secs(5), compact_task)
+        .await
+        .expect("cancelled compaction waiter was not released")
+        .expect("compaction task panicked")
+        .unwrap_err();
+    assert_eq!(compact_err.status_code(), StatusCode::Cancelled);
+    assert!(!truncate_task.is_finished());
+
+    pending_ddl_guard.release();
+    tokio::time::timeout(Duration::from_secs(5), truncate_task)
+        .await
+        .expect("queued truncate did not finish after compaction cancellation")
+        .expect("truncate task panicked")
+        .expect("queued truncate failed");
+}
+
+#[tokio::test]
+async fn test_truncate_waits_for_non_cancellable_compaction_commit() {
+    common_telemetry::init_default_ut_logging();
+    let mut env = TestEnv::new().await;
+    let region_id = RegionId::new(10, 1);
+    let gate = Arc::new(CompactionPlanningGate::new(region_id));
+    let engine = env
+        .create_engine_with(
+            MitoConfig {
+                num_workers: 1,
+                min_compaction_interval: Duration::from_secs(60 * 60),
+                ..Default::default()
+            },
+            None,
+            Some(gate.clone()),
+            None,
+        )
+        .await;
+    env.get_schema_metadata_manager()
+        .register_region_table_info(
+            region_id.table_id(),
+            "truncate_during_compaction_commit",
+            "test_catalog",
+            "test_schema",
+            None,
+            env.get_kv_backend(),
+        )
+        .await;
+    let create = CreateRequestBuilder::new()
+        .insert_option("compaction.type", "twcs")
+        .build();
+    let table_dir = create.table_dir.clone();
+    let options = create.options.clone();
+    let column_schemas = create
+        .column_metadatas
+        .iter()
+        .map(column_metadata_to_column_schema)
+        .collect::<Vec<_>>();
+    engine
+        .handle_request(region_id, RegionRequest::Create(create))
+        .await
+        .unwrap();
+    put_and_flush(&engine, region_id, &column_schemas, 0..10).await;
+    put_and_flush(&engine, region_id, &column_schemas, 5..20).await;
+    let input_file_ids = engine
+        .scanner(region_id, ScanRequest::default())
+        .await
+        .unwrap()
+        .file_ids();
+    assert_eq!(2, input_file_ids.len());
+
+    let commit_guard = gate.arm_commit();
+    let compact_engine = engine.clone();
+    let compact_task = tokio::spawn(async move {
+        compact_engine
+            .handle_request(
+                region_id,
+                RegionRequest::Compact(RegionCompactRequest::default()),
+            )
+            .await
+    });
+    tokio::time::timeout(Duration::from_secs(5), gate.wait_until_commit_entered())
+        .await
+        .expect("compaction did not reach the non-cancellable commit gate");
+
+    let truncate_engine = engine.clone();
+    let mut truncate_task = tokio::spawn(async move {
+        truncate_engine
+            .handle_request(
+                region_id,
+                RegionRequest::Truncate(RegionTruncateRequest::ByTimeRanges {
+                    time_ranges: vec![(
+                        Timestamp::new_millisecond(0),
+                        Timestamp::new_millisecond(19_000),
+                    )],
+                }),
+            )
+            .await
+    });
+    tokio::time::timeout(Duration::from_secs(5), async {
+        tokio::select! {
+            biased;
+            result = &mut truncate_task => {
+                panic!("truncate completed before compaction terminal completion: {result:?}");
+            }
+            () = gate.wait_until_cancel_requested() => {}
+        }
+    })
+    .await
+    .expect("truncate was not queued behind non-cancellable compaction");
+    assert!(!truncate_task.is_finished());
+
+    let pending_ddl_guard = gate.arm_pending_ddl_dispatch();
+    commit_guard.release();
+    tokio::time::timeout(
+        Duration::from_secs(5),
+        gate.wait_until_pending_ddl_dispatch(),
+    )
+    .await
+    .expect("compaction terminal result did not reach pending truncate dispatch");
+    tokio::time::timeout(Duration::from_secs(5), compact_task)
+        .await
+        .expect("compaction waiter was not released at terminal completion")
+        .expect("compaction task panicked")
+        .expect("compaction failed");
+    assert!(!truncate_task.is_finished());
+    let scanner = engine
+        .scanner(region_id, ScanRequest::default())
+        .await
+        .unwrap();
+    let compacted_file_ids = scanner.file_ids();
+    assert_eq!(1, compacted_file_ids.len());
+    let compacted_file_id = compacted_file_ids[0];
+    assert!(!input_file_ids.contains(&compacted_file_id));
+    assert_eq!(
+        (0..20).map(|value| value * 1000).collect::<Vec<_>>(),
+        collect_stream_ts(scanner.scan().await.unwrap()).await
+    );
+
+    pending_ddl_guard.release();
+    tokio::time::timeout(Duration::from_secs(5), truncate_task)
+        .await
+        .expect("queued truncate did not finish after compaction completion")
+        .expect("truncate task panicked")
+        .expect("queued truncate failed");
+
+    let scanner = engine
+        .scanner(region_id, ScanRequest::default())
+        .await
+        .unwrap();
+    assert!(!scanner.file_ids().contains(&compacted_file_id));
+    assert!(
+        collect_stream_ts(scanner.scan().await.unwrap())
+            .await
+            .is_empty()
+    );
+
+    engine
+        .handle_request(
+            region_id,
+            RegionRequest::Close(RegionCloseRequest::default()),
+        )
+        .await
+        .unwrap();
+    engine
+        .handle_request(
+            region_id,
+            RegionRequest::Open(RegionOpenRequest {
+                engine: String::new(),
+                table_dir,
+                path_type: PathType::Bare,
+                options,
+                skip_wal_replay: false,
+                checkpoint: None,
+                requirements: Default::default(),
+            }),
+        )
+        .await
+        .unwrap();
+    engine
+        .set_region_role(region_id, RegionRole::Leader)
+        .unwrap();
+
+    let scanner = engine
+        .scanner(region_id, ScanRequest::default())
+        .await
+        .unwrap();
+    assert!(!scanner.file_ids().contains(&compacted_file_id));
+    assert!(
+        collect_stream_ts(scanner.scan().await.unwrap())
+            .await
+            .is_empty()
+    );
+}
+
 #[tokio::test]
 async fn test_worker_shutdown_fails_picking_waiter() {
     common_telemetry::init_default_ut_logging();
diff --git a/src/mito2/src/worker/handle_truncate.rs b/src/mito2/src/worker/handle_truncate.rs
index 0867560a7b..dadc8eff54 100644
--- a/src/mito2/src/worker/handle_truncate.rs
+++ b/src/mito2/src/worker/handle_truncate.rs
@@ -19,10 +19,11 @@ use store_api::logstore::LogStore;
 use store_api::region_request::RegionTruncateRequest;
 use store_api::storage::RegionId;
 
+use crate::compaction::RequestCancelResult;
 use crate::error::RegionNotFoundSnafu;
 use crate::manifest::action::{RegionTruncate, TruncateKind};
 use crate::region::RegionLeaderState;
-use crate::request::{OptionOutputTx, TruncateResult};
+use crate::request::{DdlRequest, OptionOutputTx, SenderDdlRequest, TruncateResult};
 use crate::worker::RegionWorkerLoop;
 
 impl<S: LogStore> RegionWorkerLoop<S> {
@@ -40,6 +41,25 @@ impl<S: LogStore> RegionWorkerLoop<S> {
             }
         };
 
+        match self.compaction_scheduler.request_cancel(region_id) {
+            RequestCancelResult::CancelIssued
+            | RequestCancelResult::AlreadyCancelling
+            | RequestCancelResult::TooLateToCancel => {
+                // Safety: region is compacting or has entered the non-cancellable publish stage,
+                // keep the DDL pending until the current task finishes or acknowledges cancellation.
+                self.compaction_scheduler
+                    .add_ddl_request_to_pending(SenderDdlRequest {
+                        region_id,
+                        sender,
+                        request: DdlRequest::Truncate(req),
+                    });
+                self.listener.on_compaction_cancel_requested(region_id);
+
+                return;
+            }
+            RequestCancelResult::NotRunning => {}
+        }
+
         let version_data = region.version_control.current();
 
         match req {