diff --git a/src/mito2/src/engine.rs b/src/mito2/src/engine.rs
index 64f7576139..782c82b54a 100644
--- a/src/mito2/src/engine.rs
+++ b/src/mito2/src/engine.rs
@@ -613,8 +613,10 @@ impl MitoEngine {
                             return Vec::new();
                         }
                     };
+                    // The index file path is derived from the physical file owner. After
+                    // repartition, `entry.region_id` is only the referring region.
                     let region_index_id = RegionIndexId::new(
-                        RegionFileId::new(entry.region_id, file_id),
+                        RegionFileId::new(entry.origin_region_id, file_id),
                         index_version,
                     );
                     let context = IndexEntryContext {
diff --git a/src/mito2/src/region.rs b/src/mito2/src/region.rs
index f6d2a17bba..9d214caed3 100644
--- a/src/mito2/src/region.rs
+++ b/src/mito2/src/region.rs
@@ -601,14 +601,14 @@ impl MitoRegion {
         let memtables = &version.memtables;
         let memtable_usage = (memtables.mutable_usage() + memtables.immutables_usage()) as u64;
 
-        let sst_usage = version.ssts.sst_usage();
-        let index_usage = version.ssts.index_usage();
+        let sst_usage = version.ssts.owned_sst_usage(self.region_id);
+        let index_usage = version.ssts.owned_index_usage(self.region_id);
         let flushed_entry_id = version.flushed_entry_id;
 
         let wal_usage = self.estimated_wal_usage(memtable_usage);
         let manifest_usage = self.stats.total_manifest_size();
-        let num_rows = version.ssts.num_rows() + version.memtables.num_rows();
-        let num_files = version.ssts.num_files();
+        let num_rows = version.ssts.owned_num_rows(self.region_id) + version.memtables.num_rows();
+        let num_files = version.ssts.owned_num_files(self.region_id);
         let manifest_version = self.stats.manifest_version();
         let file_removed_cnt = self.stats.file_removed_cnt();
 
diff --git a/src/mito2/src/sst/version.rs b/src/mito2/src/sst/version.rs
index 5958cf7513..67d41a3b82 100644
--- a/src/mito2/src/sst/version.rs
+++ b/src/mito2/src/sst/version.rs
@@ -18,7 +18,7 @@ use std::fmt;
 use std::sync::Arc;
 
 use common_time::{TimeToLive, Timestamp};
-use store_api::storage::FileId;
+use store_api::storage::{FileId, RegionId};
 
 use crate::sst::file::{FileHandle, FileMeta, Level, MAX_LEVEL};
 use crate::sst::file_purger::FilePurgerRef;
@@ -106,15 +106,19 @@ impl SstVersion {
         }
     }
 
-    /// Returns the number of rows in SST files.
+    /// Returns the number of rows in SST files owned by `region_id`.
+    ///
+    /// Rows from SST files referenced from other regions, for example after
+    /// repartition, are not counted.
     /// For historical reasons, the result is not precise for old SST files.
-    pub(crate) fn num_rows(&self) -> u64 {
+    pub(crate) fn owned_num_rows(&self, region_id: RegionId) -> u64 {
         self.levels
             .iter()
             .map(|level_meta| {
                 level_meta
                     .files
                     .values()
+                    .filter(|file_handle| file_handle.region_id() == region_id)
                     .map(|file_handle| {
                         let meta = file_handle.meta_ref();
                         meta.num_rows
@@ -124,22 +128,29 @@ impl SstVersion {
             .sum()
     }
 
-    /// Returns the number of SST files.
-    pub(crate) fn num_files(&self) -> u64 {
-        self.levels
-            .iter()
-            .map(|level_meta| level_meta.files.len() as u64)
-            .sum()
-    }
-
-    /// Returns SST data files'space occupied in current version.
-    pub(crate) fn sst_usage(&self) -> u64 {
+    /// Returns the number of SST files owned by `region_id`.
+    pub(crate) fn owned_num_files(&self, region_id: RegionId) -> u64 {
         self.levels
             .iter()
             .map(|level_meta| {
                 level_meta
                     .files
                     .values()
+                    .filter(|file_handle| file_handle.region_id() == region_id)
+                    .count() as u64
+            })
+            .sum()
+    }
+
+    /// Returns the space occupied by SST data files owned by `region_id`.
+    pub(crate) fn owned_sst_usage(&self, region_id: RegionId) -> u64 {
+        self.levels
+            .iter()
+            .map(|level_meta| {
+                level_meta
+                    .files
+                    .values()
+                    .filter(|file_handle| file_handle.region_id() == region_id)
                     .map(|file_handle| {
                         let meta = file_handle.meta_ref();
                         meta.file_size
@@ -149,14 +160,15 @@ impl SstVersion {
             .sum()
     }
 
-    /// Returns SST index files'space occupied in current version.
-    pub(crate) fn index_usage(&self) -> u64 {
+    /// Returns the space occupied by SST index files owned by `region_id`.
+    pub(crate) fn owned_index_usage(&self, region_id: RegionId) -> u64 {
         self.levels
             .iter()
             .map(|level_meta| {
                 level_meta
                     .files
                     .values()
+                    .filter(|file_handle| file_handle.region_id() == region_id)
                     .map(|file_handle| {
                         let meta = file_handle.meta_ref();
                         meta.index_file_size
@@ -257,4 +269,50 @@ mod tests {
             assert!(added_files.contains_key(&f.file_id));
         });
     }
+
+    #[test]
+    fn test_usage_only_counts_owned_files() {
+        let purger = new_noop_file_purger();
+        let region_id = RegionId::new(1, 1);
+        let other_region_id = RegionId::new(1, 2);
+
+        let files = [
+            FileMeta {
+                region_id,
+                file_id: FileId::random(),
+                file_size: 100,
+                index_file_size: 10,
+                num_rows: 1,
+                ..Default::default()
+            },
+            FileMeta {
+                region_id,
+                file_id: FileId::random(),
+                file_size: 200,
+                index_file_size: 20,
+                num_rows: 2,
+                ..Default::default()
+            },
+            FileMeta {
+                region_id: other_region_id,
+                file_id: FileId::random(),
+                file_size: 300,
+                index_file_size: 30,
+                num_rows: 3,
+                ..Default::default()
+            },
+        ];
+
+        let mut version = SstVersion::new();
+        version.add_files(purger, files.iter().cloned());
+
+        assert_eq!(3, version.owned_num_rows(region_id));
+        assert_eq!(2, version.owned_num_files(region_id));
+        assert_eq!(300, version.owned_sst_usage(region_id));
+        assert_eq!(30, version.owned_index_usage(region_id));
+        assert_eq!(3, version.owned_num_rows(other_region_id));
+        assert_eq!(1, version.owned_num_files(other_region_id));
+        assert_eq!(300, version.owned_sst_usage(other_region_id));
+        assert_eq!(30, version.owned_index_usage(other_region_id));
+    }
 }
diff --git a/src/store-api/src/region_engine.rs b/src/store-api/src/region_engine.rs
index b235fcffc7..e5ab05e5e7 100644
--- a/src/store-api/src/region_engine.rs
+++ b/src/store-api/src/region_engine.rs
@@ -483,7 +483,10 @@ pub type BatchResponses = Vec<(RegionId, Result<RegionResponse, BoxedError>)>;
 /// Represents the statistics of a region.
 #[derive(Debug, Deserialize, Serialize, Default)]
 pub struct RegionStatistic {
-    /// The number of rows
+    /// The number of rows stored in SST files owned by this region plus rows in memtables.
+    ///
+    /// Rows from SST files referenced from other regions, for example after repartition,
+    /// are not counted to avoid table-level double counting when summing region statistics.
     #[serde(default)]
     pub num_rows: u64,
     /// The size of memtable in bytes.
@@ -492,11 +495,17 @@ pub struct RegionStatistic {
     pub wal_size: u64,
     /// The size of manifest in bytes.
     pub manifest_size: u64,
-    /// The size of SST data files in bytes.
+    /// The size of SST data files owned by this region in bytes.
+    ///
+    /// SST files referenced from other regions, for example after repartition, are not counted.
     pub sst_size: u64,
-    /// The num of SST files.
+    /// The number of SST files owned by this region.
+    ///
+    /// SST files referenced from other regions, for example after repartition, are not counted.
     pub sst_num: u64,
-    /// The size of SST index files in bytes.
+    /// The size of SST index files owned by this region in bytes.
+    ///
+    /// SST index files referenced from other regions, for example after repartition, are not counted.
     #[serde(default)]
     pub index_size: u64,
     /// The details of the region.