diff --git a/src/mito2/src/compaction.rs b/src/mito2/src/compaction.rs
index 0a2ec880d8a4..ffff9bebe4b8 100644
--- a/src/mito2/src/compaction.rs
+++ b/src/mito2/src/compaction.rs
@@ -116,6 +116,8 @@ impl CompactionScheduler {
 
         // The region can compact directly.
         let request = status.new_compaction_request(self.request_sender.clone(), waiter);
+        // Mark the region as compacting.
+        status.compacting = true;
         self.schedule_compaction_request(request)
     }
 
diff --git a/src/mito2/src/compaction/twcs.rs b/src/mito2/src/compaction/twcs.rs
index f02884381be5..9812e2c00f5d 100644
--- a/src/mito2/src/compaction/twcs.rs
+++ b/src/mito2/src/compaction/twcs.rs
@@ -156,8 +156,6 @@ impl Picker for TwcsPicker {
         let outputs = self.build_output(&windows, active_window, time_window_size);
 
         if outputs.is_empty() && expired_ssts.is_empty() {
-            // FIXME(yingwen): Need to remove the region from the scheduler.
-
             // Nothing to compact, we are done. Notifies all waiters as we consume the compaction request.
             for waiter in waiters {
                 waiter.send(Ok(Output::AffectedRows(0)));
diff --git a/src/mito2/src/engine/compaction_test.rs b/src/mito2/src/engine/compaction_test.rs
index 9c196d78b900..9a88ecbc4989 100644
--- a/src/mito2/src/engine/compaction_test.rs
+++ b/src/mito2/src/engine/compaction_test.rs
@@ -121,10 +121,12 @@ async fn test_compaction_region() {
         .handle_request(region_id, RegionRequest::Create(request))
         .await
         .unwrap();
+    // Flush 5 SSTs for compaction.
     put_and_flush(&engine, region_id, &column_schemas, 0..10).await;
     put_and_flush(&engine, region_id, &column_schemas, 10..20).await;
     put_and_flush(&engine, region_id, &column_schemas, 20..30).await;
-    delete_and_flush(&engine, region_id, &column_schemas, 25..30).await;
+    delete_and_flush(&engine, region_id, &column_schemas, 15..30).await;
+    put_and_flush(&engine, region_id, &column_schemas, 15..25).await;
 
     let output = engine
         .handle_request(region_id, RegionRequest::Compact(RegionCompactRequest {}))
@@ -132,10 +134,14 @@ async fn test_compaction_region() {
         .unwrap();
     assert!(matches!(output, Output::AffectedRows(0)));
 
-    let stream = engine
-        .handle_query(region_id, ScanRequest::default())
-        .await
-        .unwrap();
+    let scanner = engine.scanner(region_id, ScanRequest::default()).unwrap();
+    assert_eq!(
+        1,
+        scanner.num_files(),
+        "unexpected files: {:?}",
+        scanner.file_ids()
+    );
+    let stream = scanner.scan().await.unwrap();
 
     let vec = collect_stream_ts(stream).await;
     assert_eq!((0..25).map(|v| v * 1000).collect::<Vec<_>>(), vec);
diff --git a/src/mito2/src/read/scan_region.rs b/src/mito2/src/read/scan_region.rs
index 752821834e94..be8b318d83ff 100644
--- a/src/mito2/src/read/scan_region.rs
+++ b/src/mito2/src/read/scan_region.rs
@@ -59,6 +59,13 @@ impl Scanner {
             Scanner::Seq(seq_scan) => seq_scan.num_memtables(),
         }
     }
+
+    /// Returns SST file ids to scan.
+    pub(crate) fn file_ids(&self) -> Vec<crate::sst::file::FileId> {
+        match self {
+            Scanner::Seq(seq_scan) => seq_scan.file_ids(),
+        }
+    }
 }
 
 #[cfg_attr(doc, aquamarine::aquamarine)]
diff --git a/src/mito2/src/read/seq_scan.rs b/src/mito2/src/read/seq_scan.rs
index 28e5249fecc8..148cb3777142 100644
--- a/src/mito2/src/read/seq_scan.rs
+++ b/src/mito2/src/read/seq_scan.rs
@@ -156,4 +156,9 @@ impl SeqScan {
     pub(crate) fn num_files(&self) -> usize {
         self.files.len()
     }
+
+    /// Returns SST file ids to scan.
+    pub(crate) fn file_ids(&self) -> Vec<crate::sst::file::FileId> {
+        self.files.iter().map(|file| file.file_id()).collect()
+    }
 }