diff --git a/internal/pkg/store/setup.go b/internal/pkg/store/setup.go
index 260898db8b..adda40ed7a 100644
--- a/internal/pkg/store/setup.go
+++ b/internal/pkg/store/setup.go
@@ -42,10 +42,10 @@ func SetupDefault(dataDir string) error {
 		Fdb: definition.FdbConfig{},
 	}
 
-	return Setup(c)
+	return Setup(c, false)
 }
 
-func SetupWithConfig(sc *StoreConf) error {
+func SetupWithConfig(sc *StoreConf, setupCheckpointDB bool) error {
 	c := definition.Config{
 		Type:         sc.Type,
 		ExtStateType: sc.ExtStateType,
@@ -54,15 +54,29 @@ func SetupWithConfig(sc *StoreConf) error {
 		Fdb:          sc.FdbConfig,
 		Pebble:       sc.PebbleConfig,
 	}
-	return Setup(c)
+	return Setup(c, setupCheckpointDB)
 }
 
-func Setup(config definition.Config) error {
+func Setup(config definition.Config, setupCheckpointDB bool) error {
 	s, err := newStores(config, "sqliteKV.db")
 	if err != nil {
 		return err
 	}
 	globalStores = s
+	if setupCheckpointDB {
+		s, err = newStores(config, "checkpoint.db")
+		if err != nil {
+			return err
+		}
+		checkpointStores = s
+		db, err := checkpointStores.GetKV("init_checkpointdb")
+		if err != nil {
+			checkpointStores = nil
+		} else {
+			// write sth to ensure checkpoint.db created
+			db.Set("init", "init")
+		}
+	}
 	s, err = newStores(config, "cache.db")
 	if err != nil {
 		return err
diff --git a/internal/pkg/store/stores.go b/internal/pkg/store/stores.go
index fbc0759fb3..e468d7a96b 100644
--- a/internal/pkg/store/stores.go
+++ b/internal/pkg/store/stores.go
@@ -31,9 +31,10 @@ var (
 	storeBuilders = map[string]StoreCreator{
 		"sqlite": sql.BuildStores,
 	}
-	globalStores   *stores = nil
-	cacheStores    *stores = nil
-	extStateStores *stores = nil
+	globalStores     *stores = nil
+	cacheStores      *stores = nil
+	extStateStores   *stores = nil
+	checkpointStores *stores = nil
 
 	TraceStores sql.Database
 )
@@ -154,6 +155,9 @@ func GetKV(table string) (kv.KeyValue, error) {
 }
 
 func GetTS(table string) (kv.Tskv, error) {
+	if checkpointStores != nil {
+		return checkpointStores.GetTS(table)
+	}
 	if globalStores == nil {
 		return nil, fmt.Errorf("global stores are not initialized")
 	}
@@ -161,6 +165,10 @@ func GetTS(table string) (kv.Tskv, error) {
 }
 
 func DropTS(table string) error {
+	if checkpointStores != nil {
+		checkpointStores.DropTS(table)
+		return nil
+	}
 	if globalStores == nil {
 		return fmt.Errorf("global stores are not initialized")
 	}
diff --git a/internal/server/server.go b/internal/server/server.go
index 151059dde5..8a81fd61b9 100644
--- a/internal/server/server.go
+++ b/internal/server/server.go
@@ -140,10 +140,34 @@ func getStoreConfigByKuiperConfig(c *model.KuiperConf) (*store.StoreConf, error)
 	return sc, nil
 }
 
+func canSetupCheckpointDB() (setup bool) {
+	s, err := conf.GetDataLoc()
+	if err != nil {
+		return false
+	}
+	_, err = os.Stat(filepath.Join(s, "checkpoint.db"))
+	// checkpoint.db already exists, setup it.
+	if err == nil {
+		return true
+	}
+	_, err = os.Stat(filepath.Join(s, "sqliteKV.db"))
+	if err != nil {
+		// sqliteKV.db not exists, setup checkpoint.db.
+		if os.IsNotExist(err) {
+			return true
+		}
+		// unexpected error happened
+		return false
+	}
+	// sqliteKV.db exists/ checkpoint.db not exists, don't setup.
+	return false
+}
+
 func StartUp(Version string) {
 	version = Version
 	startTimeStamp = time.Now().Unix()
 	createPaths()
+	needSetup := canSetupCheckpointDB()
 	conf.SetupEnv()
 	conf.InitConf()
 	if modules.ConfHook != nil {
@@ -184,7 +208,7 @@ func StartUp(Version string) {
 	if err != nil {
 		panic(err)
 	}
-	err = store.SetupWithConfig(sc)
+	err = store.SetupWithConfig(sc, needSetup)
 	if err != nil {
 		panic(err)
 	}