diff --git a/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink.go b/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink.go
index c4e8d84e01b..42d67f05470 100644
--- a/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink.go
+++ b/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink.go
@@ -64,7 +64,7 @@ func newDDLSink(ctx context.Context,
 	changefeedID model.ChangeFeedID,
 	sinkURI *url.URL,
 	replicaConfig *config.ReplicaConfig,
-	cleanupJob func(),
+	cleanupJobs []func(),
 ) (*DDLSink, error) {
 	// create cloud storage config and then apply the params of sinkURI to it.
 	cfg := cloudstorage.NewConfig()
@@ -89,10 +89,13 @@ func newDDLSink(ctx context.Context,
 	// Note: It is intended to run the cleanup goroutine in the background.
 	// we don't wait for it to finish since the gourotine would be stuck if
 	// the downstream is abnormal, especially when the downstream is a nfs.
-	if cleanupJob == nil {
-		cleanupJob = d.runCleanup(ctx)
+	if cleanupJobs == nil {
+		cleanupJobs, err = d.runCleanup(ctx, sinkURI)
+		if err != nil {
+			return nil, err
+		}
 	}
-	go d.bgCleanup(ctx, cleanupJob)
+	go d.bgCleanup(ctx, cleanupJobs)
 	return d, nil
 }
 
@@ -158,7 +161,7 @@ func (d *DDLSink) WriteCheckpointTs(ctx context.Context,
 	return errors.Trace(err)
 }
 
-func (d *DDLSink) bgCleanup(ctx context.Context, cleanupJob func()) {
+func (d *DDLSink) bgCleanup(ctx context.Context, cleanupJobs []func()) {
 	if d.cfg.DateSeparator != config.DateSeparatorDay.String() || d.cfg.FileExpirationDays <= 0 {
 		log.Info("skip cleanup expired files for storage sink",
 			zap.String("namespace", d.id.Namespace),
@@ -169,7 +172,9 @@ func (d *DDLSink) bgCleanup(ctx context.Context, cleanupJob func()) {
 	}
 
 	clenupCron := cron.New()
-	clenupCron.AddFunc(d.cfg.FileCleanupCronSpec, cleanupJob)
+	for _, job := range cleanupJobs {
+		clenupCron.AddFunc(d.cfg.FileCleanupCronSpec, job)
+	}
 	clenupCron.Start()
 	defer clenupCron.Stop()
 	log.Info("start schedule cleanup expired files for storage sink",
@@ -186,9 +191,34 @@ func (d *DDLSink) bgCleanup(ctx context.Context, cleanupJob func()) {
 		zap.Error(ctx.Err()))
 }
 
-func (d *DDLSink) runCleanup(ctx context.Context) func() {
+func (d *DDLSink) runCleanup(ctx context.Context, uri *url.URL) ([]func(), error) {
+	ret := []func(){}
+	if uri.Scheme == "file" || uri.Scheme == "local" || uri.Scheme == "" {
+		ret = append(ret, func() {
+			checkpointTs := d.lastCheckpointTs.Load()
+			start := time.Now()
+			cnt, err := cloudstorage.RemoveEmptyDirs(ctx, d.id, uri.Path)
+			if err != nil {
+				log.Error("failed to remove empty dirs",
+					zap.String("namespace", d.id.Namespace),
+					zap.String("changefeedID", d.id.ID),
+					zap.Uint64("checkpointTs", checkpointTs),
+					zap.Duration("cost", time.Since(start)),
+					zap.Error(err),
+				)
+				return
+			}
+			log.Info("remove empty dirs",
+				zap.String("namespace", d.id.Namespace),
+				zap.String("changefeedID", d.id.ID),
+				zap.Uint64("checkpointTs", checkpointTs),
+				zap.Uint64("count", cnt),
+				zap.Duration("cost", time.Since(start)))
+		})
+	}
+
 	isCleanupRunning := atomic.Bool{}
-	return func() {
+	ret = append(ret, func() {
 		if !isCleanupRunning.CompareAndSwap(false, true) {
 			log.Warn("cleanup expired files is already running, skip this round",
 				zap.String("namespace", d.id.Namespace),
@@ -199,7 +229,7 @@ func (d *DDLSink) runCleanup(ctx context.Context) func() {
 		defer isCleanupRunning.Store(false)
 		start := time.Now()
 		checkpointTs := d.lastCheckpointTs.Load()
-		cnt, err := cloudstorage.RemoveExpiredFiles(ctx, d.storage, d.cfg, checkpointTs)
+		cnt, err := cloudstorage.RemoveExpiredFiles(ctx, d.id, d.storage, d.cfg, checkpointTs)
 		if err != nil {
 			log.Error("failed to remove expired files",
 				zap.String("namespace", d.id.Namespace),
@@ -217,7 +247,8 @@ func (d *DDLSink) runCleanup(ctx context.Context) func() {
 			zap.Uint64("checkpointTs", checkpointTs),
 			zap.Uint64("count", cnt),
 			zap.Duration("cost", time.Since(start)))
-	}
+	})
+	return ret, nil
 }
 
 // Close closes the sink.
diff --git a/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink_test.go b/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink_test.go
index b4cc70ae47b..f0fbe8475d0 100644
--- a/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink_test.go
+++ b/cdc/sink/ddlsink/cloudstorage/cloud_storage_ddl_sink_test.go
@@ -159,10 +159,12 @@ func TestCleanupExpiredFiles(t *testing.T) {
 	require.Nil(t, err)
 
 	cnt := 0
-	cleanupJob := func() {
-		cnt++
+	cleanupJobs := []func(){
+		func() {
+			cnt++
+		},
 	}
-	sink, err := newDDLSink(ctx, model.DefaultChangeFeedID("test"), sinkURI, replicaConfig, cleanupJob)
+	sink, err := newDDLSink(ctx, model.DefaultChangeFeedID("test"), sinkURI, replicaConfig, cleanupJobs)
 	require.Nil(t, err)
 
 	_ = sink
diff --git a/pkg/sink/cloudstorage/path.go b/pkg/sink/cloudstorage/path.go
index 628dabb7d3e..d792845d0cd 100644
--- a/pkg/sink/cloudstorage/path.go
+++ b/pkg/sink/cloudstorage/path.go
@@ -17,7 +17,10 @@ import (
 	"context"
 	"fmt"
 	"io"
+	"io/fs"
+	"os"
 	"path"
+	"path/filepath"
 	"regexp"
 	"strconv"
 	"strings"
@@ -412,6 +415,7 @@ var dateSeparatorDayRegexp *regexp.Regexp
 // RemoveExpiredFiles removes expired files from external storage.
 func RemoveExpiredFiles(
 	ctx context.Context,
+	_ model.ChangeFeedID,
 	storage storage.ExternalStorage,
 	cfg *Config,
 	checkpointTs model.Ts,
@@ -439,3 +443,35 @@ func RemoveExpiredFiles(
 	}, nil)
 	return cnt, err
 }
+
+func RemoveEmptyDirs(
+	ctx context.Context,
+	id model.ChangeFeedID,
+	target string,
+) (uint64, error) {
+	cnt := uint64(0)
+	err := filepath.Walk(target, func(path string, info fs.FileInfo, err error) error {
+		if os.IsNotExist(err) || path == target || info == nil {
+			// if path not exists, we should return nil to continue.
+			return nil
+		}
+		if err != nil {
+			return err
+		}
+		if info.IsDir() {
+			files, err := os.ReadDir(path)
+			if err == nil && len(files) == 0 {
+				log.Debug("Deleting empty directory",
+					zap.String("namespace", id.Namespace),
+					zap.String("changeFeedID", id.ID),
+					zap.String("path", path))
+				os.Remove(path)
+				cnt++
+				return filepath.SkipDir
+			}
+		}
+		return nil
+	})
+
+	return cnt, err
+}
diff --git a/pkg/sink/cloudstorage/path_test.go b/pkg/sink/cloudstorage/path_test.go
index 4dfa67d1060..8162dbb61b5 100644
--- a/pkg/sink/cloudstorage/path_test.go
+++ b/pkg/sink/cloudstorage/path_test.go
@@ -410,7 +410,7 @@ func TestRemoveExpiredFilesWithoutPartition(t *testing.T) {
 
 	currTime := time.Date(2021, 1, 3, 0, 0, 0, 0, time.UTC)
 	checkpointTs := oracle.GoTimeToTS(currTime)
-	cnt, err := RemoveExpiredFiles(ctx, storage, cfg, checkpointTs)
+	cnt, err := RemoveExpiredFiles(ctx, model.ChangeFeedID{}, storage, cfg, checkpointTs)
 	require.NoError(t, err)
 	require.Equal(t, uint64(16), cnt)
 }
diff --git a/tests/integration_tests/storage_cleanup/run.sh b/tests/integration_tests/storage_cleanup/run.sh
index 90e7f5849c1..833fbc05308 100644
--- a/tests/integration_tests/storage_cleanup/run.sh
+++ b/tests/integration_tests/storage_cleanup/run.sh
@@ -8,6 +8,47 @@ WORK_DIR=$OUT_DIR/$TEST_NAME
 CDC_BINARY=cdc.test
 SINK_TYPE=$1
 
+function generate_single_table_files() {
+	local workdir=$1
+	local bucket=$2
+	local schema=$3
+	local table=$4
+	local day=$5
+	local file_cnt=$6
+
+	table_dir=$workdir/$bucket/$schema/$table/$day
+	mkdir -p $table_dir
+	for i in $(seq 1 $file_cnt); do
+		touch $table_dir/$i.data
+	done
+
+	mkdir -p $table_dir/meta
+	touch $table_dir/meta/CDC.index
+}
+
+function generate_historic_files() {
+	local target_bucket="storage_test"
+	# historic files of table in schema.sql
+	generate_single_table_files $WORK_DIR $target_bucket test multi_data_type 2022-01-01 10
+	generate_single_table_files $WORK_DIR $target_bucket test multi_charset 2022-01-02 10
+	generate_single_table_files $WORK_DIR $target_bucket test binary_columns 2022-01-03 10
+
+	# historic files of tables in test but not in schema.sql
+	generate_single_table_files $WORK_DIR $target_bucket test multi_data_type_dummy 2022-01-01 10
+	generate_single_table_files $WORK_DIR $target_bucket test multi_charset_dummy 2022-01-02 10
+	generate_single_table_files $WORK_DIR $target_bucket test binary_columns_dummy 2022-01-03 10
+
+	# historic files of table belongs to different schema
+	generate_single_table_files $WORK_DIR $target_bucket test2 multi_data_type 2022-01-01 10
+	generate_single_table_files $WORK_DIR $target_bucket test2 multi_charset 2022-01-02 10
+	generate_single_table_files $WORK_DIR $target_bucket test2 binary_columns 2022-01-03 10
+
+	# historic files in different bucket, which should not be cleaned
+	generate_single_table_files $WORK_DIR storage_test2 test multi_data_type 2022-01-01 10
+	generate_single_table_files $WORK_DIR storage_test2 test multi_charset 2022-01-02 10
+	generate_single_table_files $WORK_DIR storage_test2 test binary_columns 2022-01-03 10
+}
+
 function run() {
 	if [ "$SINK_TYPE" != "storage" ]; then
 		return
@@ -18,6 +59,11 @@ function run() {
 	cd $WORK_DIR
 	run_cdc_server --workdir $WORK_DIR --binary $CDC_BINARY
 
+	generate_historic_files
+
+	# wait input
+	read -p "Press enter to continue"
+
 	SINK_URI="file://$WORK_DIR/storage_test?flush-interval=5s"
 	run_cdc_cli changefeed create --sink-uri="$SINK_URI" --config=$CUR/conf/changefeed.toml