diff --git a/config/config.md b/config/config.md
index 7385c8efb0..16384b406f 100644
--- a/config/config.md
+++ b/config/config.md
@@ -170,7 +170,7 @@
 | `storage.http_client.timeout` | String | `30s` | The total request timeout, applied from when the request starts connecting until the response body has finished.<br/>Also considered a total deadline. |
 | `storage.http_client.pool_idle_timeout` | String | `90s` | The timeout for idle sockets being kept-alive. |
 | `storage.http_client.skip_ssl_validation` | Bool | `false` | To skip the ssl verification<br/>**Security Notice**: Setting `skip_ssl_validation = true` disables certificate verification, making connections vulnerable to man-in-the-middle attacks. Only use this in development or trusted private networks. |
-| `[[region_engine]]` | -- | -- | The region engine options. You can configure multiple region engines. |
+| `[[region_engine]]` | -- | -- | The region engine options. You can configure multiple region engines.<br/>Each engine type (mito, file, metric) may appear only once; duplicates cause startup to fail. |
 | `region_engine.mito` | -- | -- | The Mito engine options. |
 | `region_engine.mito.num_workers` | Integer | `8` | Number of region workers. |
 | `region_engine.mito.worker_channel_size` | Integer | `128` | Request channel size of each worker. |
@@ -631,7 +631,7 @@
 | `storage.http_client.timeout` | String | `30s` | The total request timeout, applied from when the request starts connecting until the response body has finished.<br/>Also considered a total deadline. |
 | `storage.http_client.pool_idle_timeout` | String | `90s` | The timeout for idle sockets being kept-alive. |
 | `storage.http_client.skip_ssl_validation` | Bool | `false` | To skip the ssl verification<br/>**Security Notice**: Setting `skip_ssl_validation = true` disables certificate verification, making connections vulnerable to man-in-the-middle attacks. Only use this in development or trusted private networks. |
-| `[[region_engine]]` | -- | -- | The region engine options. You can configure multiple region engines. |
+| `[[region_engine]]` | -- | -- | The region engine options. You can configure multiple region engines.<br/>Each engine type (mito, file, metric) may appear only once; duplicates cause startup to fail. |
 | `region_engine.mito` | -- | -- | The Mito engine options. |
 | `region_engine.mito.num_workers` | Integer | `8` | Number of region workers. |
 | `region_engine.mito.worker_channel_size` | Integer | `128` | Request channel size of each worker. |
diff --git a/config/datanode.example.toml b/config/datanode.example.toml
index f99e1e124f..45baaefbdf 100644
--- a/config/datanode.example.toml
+++ b/config/datanode.example.toml
@@ -464,6 +464,7 @@ skip_ssl_validation = false
 # endpoint = "https://storage.googleapis.com"
 
 ## The region engine options. You can configure multiple region engines.
+## Each engine type (mito, file, metric) may appear only once; duplicates cause startup to fail.
 [[region_engine]]
 
 ## The Mito engine options.
diff --git a/config/standalone.example.toml b/config/standalone.example.toml
index cc4be3f593..e59e7ba1b4 100644
--- a/config/standalone.example.toml
+++ b/config/standalone.example.toml
@@ -674,6 +674,7 @@ skip_ssl_validation = false
 # endpoint = "https://storage.googleapis.com"
 
 ## The region engine options. You can configure multiple region engines.
+## Each engine type (mito, file, metric) may appear only once; duplicates cause startup to fail.
 [[region_engine]]
 
 ## The Mito engine options.
diff --git a/src/datanode/src/datanode.rs b/src/datanode/src/datanode.rs
index 15e83fc1c7..ae4b0723e1 100644
--- a/src/datanode/src/datanode.rs
+++ b/src/datanode/src/datanode.rs
@@ -14,11 +14,13 @@
 
 //! Datanode implementation.
 
+use std::collections::HashMap;
 use std::path::Path;
 use std::sync::Arc;
 use std::time::{Duration, Instant};
 
 use common_base::Plugins;
+use common_catalog::consts::{FILE_ENGINE, METRIC_ENGINE, MITO_ENGINE};
 use common_datasource::object_store::LocalFileAccess;
 use common_error::ext::BoxedError;
 use common_greptimedb_telemetry::GreptimeDBTelemetryTask;
@@ -63,9 +65,10 @@ use tokio::sync::Notify;
 use crate::config::{DatanodeOptions, RegionEngineConfig, StorageConfig};
 use crate::error::{
     self, BuildDatanodeSnafu, BuildMetricEngineSnafu, BuildMitoEngineSnafu, CreateDirSnafu,
-    DataFusionSnafu, GetMetadataSnafu, InvalidObjectStoreWalConfigSnafu, MissingCacheSnafu,
-    MissingNodeIdSnafu, ObjectStoreWalNotSupportedSnafu, OpenLogStoreSnafu, Result,
-    ShutdownInstanceSnafu, ShutdownServerSnafu, StartServerSnafu,
+    DataFusionSnafu, DuplicateRegionEngineConfigSnafu, GetMetadataSnafu,
+    InvalidObjectStoreWalConfigSnafu, MissingCacheSnafu, MissingNodeIdSnafu,
+    ObjectStoreWalNotSupportedSnafu, OpenLogStoreSnafu, Result, ShutdownInstanceSnafu,
+    ShutdownServerSnafu, StartServerSnafu,
 };
 use crate::event_listener::{
     NoopRegionServerEventListener, RegionServerEventListenerRef, RegionServerEventReceiver,
@@ -253,6 +256,7 @@ impl DatanodeBuilder {
     }
 
     pub async fn build(mut self) -> Result<Datanode> {
+        validate_region_engine_config(&self.opts.region_engine)?;
         let node_id = self.opts.node_id.context(MissingNodeIdSnafu)?;
         set_default_prefix(self.opts.default_column_prefix.as_deref())
             .map_err(BoxedError::new)
@@ -710,6 +714,27 @@ impl DatanodeBuilder {
     }
 }
 
+/// Rejects repeated engine types before their configs can silently overwrite each other.
+fn validate_region_engine_config(configs: &[RegionEngineConfig]) -> Result<()> {
+    let mut engine_indices = HashMap::new();
+    for (index, config) in configs.iter().enumerate() {
+        let engine = match config {
+            RegionEngineConfig::Mito(_) => MITO_ENGINE,
+            RegionEngineConfig::File(_) => FILE_ENGINE,
+            RegionEngineConfig::Metric(_) => METRIC_ENGINE,
+        };
+        if let Some(first_index) = engine_indices.insert(engine, index) {
+            return DuplicateRegionEngineConfigSnafu {
+                engine,
+                first_index,
+                duplicate_index: index,
+            }
+            .fail();
+        }
+    }
+    Ok(())
+}
+
 /// Rejects an object store WAL config the log store cannot run on.
 fn validate_object_store_wal_config(config: &ObjectStoreWalConfig) -> Result<()> {
     let prefix = config.prefix.trim();
@@ -879,6 +904,7 @@ async fn open_all_regions(
 mod tests {
     use std::assert_matches;
     use std::collections::{BTreeMap, HashMap};
+    use std::io::Write;
     use std::path::Path;
     use std::sync::Arc;
     use std::time::Duration;
@@ -886,6 +912,7 @@ mod tests {
     use cache::build_datanode_cache_registry;
     use common_base::Plugins;
     use common_base::readable_size::ReadableSize;
+    use common_config::Configurable;
     use common_error::ext::ErrorExt;
     use common_error::status_code::StatusCode;
     use common_meta::cache::LayeredCacheRegistryBuilder;
@@ -893,15 +920,17 @@ mod tests {
     use common_meta::key::datanode_table::DatanodeTableManager;
     use common_meta::kv_backend::KvBackendRef;
     use common_meta::kv_backend::memory::MemoryKvBackend;
-    use common_test_util::temp_dir::create_temp_dir;
+    use common_test_util::temp_dir::{create_named_temp_file, create_temp_dir};
     use common_wal::config::DatanodeWalConfig;
     use common_wal::config::object_store::{ObjectStoreWalConfig, STANDALONE_GENERATION};
     use mito2::engine::MITO_ENGINE_NAME;
     use store_api::region_request::RegionRequest;
     use store_api::storage::RegionId;
 
-    use crate::config::DatanodeOptions;
-    use crate::datanode::{DatanodeBuilder, validate_object_store_wal_config};
+    use crate::config::{DatanodeOptions, RegionEngineConfig};
+    use crate::datanode::{
+        DatanodeBuilder, validate_object_store_wal_config, validate_region_engine_config,
+    };
     use crate::error::Error;
     use crate::tests::{MockRegionEngine, mock_region_server};
 
@@ -1014,6 +1043,74 @@ mod tests {
         std::fs::read_dir(dir).unwrap().next().is_none()
     }
 
+    #[test]
+    fn test_validate_unique_region_engine_config() {
+        let mut opts = DatanodeOptions::default();
+        validate_region_engine_config(&opts.region_engine).unwrap();
+
+        opts.region_engine
+            .push(RegionEngineConfig::Metric(Default::default()));
+        validate_region_engine_config(&opts.region_engine).unwrap();
+
+        // Omitted engines still use their defaults during engine construction.
+        validate_region_engine_config(&[]).unwrap();
+    }
+
+    #[tokio::test]
+    async fn test_build_rejects_duplicate_region_engine_config() {
+        for (engine, first_index) in [("mito", 0), ("file", 1), ("metric", 2)] {
+            let mut file = create_named_temp_file();
+            write!(
+                file,
+                r#"
+                [[region_engine]]
+                [region_engine.mito]
+                global_write_buffer_size = "4GiB"
+                min_compaction_interval = "600s"
+
+                [[region_engine]]
+                [region_engine.file]
+
+                [[region_engine]]
+                [region_engine.metric]
+
+                [[region_engine]]
+                [region_engine.{engine}]
+                "#
+            )
+            .unwrap();
+            let opts = DatanodeOptions::load_layered_options(
+                Some(file.path().to_str().unwrap()),
+                "DATANODE_DUPLICATE_REGION_ENGINE_UT",
+            )
+            .unwrap();
+            let data_home = create_temp_dir("duplicate-region-engine-config");
+            let mut builder = datanode_builder(
+                data_home.path().to_str().unwrap(),
+                DatanodeWalConfig::default(),
+                Arc::new(MemoryKvBackend::new()),
+            );
+            builder.opts.region_engine = opts.region_engine;
+            let err = build_err(builder).await;
+
+            let Error::DuplicateRegionEngineConfig {
+                engine: actual_engine,
+                first_index: actual_first_index,
+                duplicate_index,
+                ..
+            } = &err
+            else {
+                panic!("unexpected error for {engine}: {err:?}");
+            };
+            assert_eq!(*actual_engine, engine);
+            assert_eq!(*actual_first_index, first_index);
+            assert_eq!(*duplicate_index, 3);
+            assert_eq!(err.status_code(), StatusCode::InvalidArguments);
+            // Rejected before the builder creates any storage or log store.
+            assert!(is_empty_dir(data_home.path()));
+        }
+    }
+
     #[tokio::test]
     async fn test_build_rejects_invalid_object_store_wal_config() {
         let cases = [
diff --git a/src/datanode/src/error.rs b/src/datanode/src/error.rs
index c391efffcf..b62708aa34 100644
--- a/src/datanode/src/error.rs
+++ b/src/datanode/src/error.rs
@@ -299,6 +299,17 @@ pub enum Error {
         location: Location,
     },
 
+    #[snafu(display(
+        "Duplicate region engine config '{engine}' at region_engine[{first_index}] and region_engine[{duplicate_index}] (indices are zero-based); each engine type may be configured only once"
+    ))]
+    DuplicateRegionEngineConfig {
+        engine: &'static str,
+        first_index: usize,
+        duplicate_index: usize,
+        #[snafu(implicit)]
+        location: Location,
+    },
+
     #[snafu(display("Invalid object store WAL config, {} = {:?}: {}", field, value, reason))]
     InvalidObjectStoreWalConfig {
         field: &'static str,
@@ -486,6 +497,7 @@ impl ErrorExt for Error {
             | GcConfigMismatch { .. }
             | ParseAddr { .. }
             | TomlFormat { .. }
+            | DuplicateRegionEngineConfig { .. }
             | InvalidObjectStoreWalConfig { .. }
             | BuildDatanode { .. } => StatusCode::InvalidArguments,