diff --git a/server/cluster/cluster.go b/server/cluster/cluster.go
index 54085ef533ba..33ed5711ac5c 100644
--- a/server/cluster/cluster.go
+++ b/server/cluster/cluster.go
@@ -427,25 +427,25 @@ func (c *RaftCluster) runStoreConfigSync() {
 	defer c.wg.Done()
 
 	var (
-		synced, switchRaftV2Config, isLastSynced bool
-		stores                                   = c.GetStores()
+		synced, switchRaftV2Config, needPersist bool
+		stores                                  = c.GetStores()
 	)
 	// Start the ticker with a second-level timer to accelerate
 	// the bootstrap stage.
 	ticker := time.NewTicker(time.Minute)
 	defer ticker.Stop()
 	for {
-		synced, switchRaftV2Config = c.syncStoreConfig(stores)
+		synced, switchRaftV2Config, needPersist = c.syncStoreConfig(stores)
 		if switchRaftV2Config {
 			if err := c.opt.SwitchRaftV2(c.GetStorage()); err != nil {
 				log.Warn("store config persisted failed", zap.Error(err))
 			}
 		}
-		isLastSynced = synced
 		// Update the stores if the synchronization is not completed.
 		if !synced {
 			stores = c.GetStores()
-		} else if !isLastSynced && synced {
+		}
+		if needPersist {
 			if err := c.opt.Persist(c.storage); err != nil {
 				log.Warn("store config persisted failed", zap.Error(err))
 			}
@@ -462,7 +462,8 @@ func (c *RaftCluster) runStoreConfigSync() {
 // syncStoreConfig syncs the store config from TiKV.
 //   - `synced` is true if sync config from one tikv.
 //   - `switchRaftV2` is true if the config of tikv engine is change to raft-kv2.
-func (c *RaftCluster) syncStoreConfig(stores []*core.StoreInfo) (synced bool, switchRaftV2 bool) {
+func (c *RaftCluster) syncStoreConfig(stores []*core.StoreInfo) (synced bool, switchRaftV2 bool, needPersist bool) {
+	var err error
 	for index := 0; index < len(stores); index++ {
 		select {
 		case <-c.ctx.Done():
@@ -482,7 +483,7 @@ func (c *RaftCluster) syncStoreConfig(stores []*core.StoreInfo) (synced bool, sw
 		}
 		// it will try next store if the current store is failed.
 		address := netutil.ResolveLoopBackAddr(stores[index].GetStatusAddress(), stores[index].GetAddress())
-		switchRaftV2, err := c.observeStoreConfig(c.ctx, address)
+		switchRaftV2, needPersist, err = c.observeStoreConfig(c.ctx, address)
 		if err != nil {
 			// delete the store if it is failed and retry next store.
 			stores = append(stores[:index], stores[index+1:]...)
@@ -495,34 +496,35 @@ func (c *RaftCluster) syncStoreConfig(stores []*core.StoreInfo) (synced bool, sw
 		}
 		storeSyncConfigEvent.WithLabelValues(address, "succ").Inc()
 
-		return true, switchRaftV2
+		return true, switchRaftV2, needPersist
 	}
-	return false, false
+	return false, false, needPersist
 }
 
 // observeStoreConfig is used to observe the store config changes and
 // return whether if the new config changes the engine to raft-kv2.
-func (c *RaftCluster) observeStoreConfig(ctx context.Context, address string) (bool, error) {
+func (c *RaftCluster) observeStoreConfig(ctx context.Context, address string) (switchRaftV2 bool, needPersist bool, err error) {
 	cfg, err := c.fetchStoreConfigFromTiKV(ctx, address)
 	if err != nil {
-		return false, err
+		return false, false, err
 	}
 	oldCfg := c.opt.GetStoreConfig()
 	if cfg == nil || oldCfg.Equal(cfg) {
-		return false, nil
+		return false, false, nil
 	}
 	log.Info("sync the store config successful",
 		zap.String("store-address", address),
 		zap.String("store-config", cfg.String()),
 		zap.String("old-config", oldCfg.String()))
-	return c.updateStoreConfig(oldCfg, cfg)
+	return c.updateStoreConfig(oldCfg, cfg), true, nil
 }
 
 // updateStoreConfig updates the store config. This is extracted for testing.
-func (c *RaftCluster) updateStoreConfig(oldCfg, cfg *sc.StoreConfig) (bool, error) {
+func (c *RaftCluster) updateStoreConfig(oldCfg, cfg *sc.StoreConfig) (switchRaftV2 bool) {
 	cfg.Adjust()
 	c.opt.SetStoreConfig(cfg)
-	return oldCfg.Storage.Engine != sc.RaftstoreV2 && cfg.Storage.Engine == sc.RaftstoreV2, nil
+	switchRaftV2 = oldCfg.Storage.Engine != sc.RaftstoreV2 && cfg.Storage.Engine == sc.RaftstoreV2
+	return
 }
 
 // fetchStoreConfigFromTiKV tries to fetch the config from the TiKV store URL.
diff --git a/server/cluster/cluster_test.go b/server/cluster/cluster_test.go
index aa826e344069..5cfec7d42302 100644
--- a/server/cluster/cluster_test.go
+++ b/server/cluster/cluster_test.go
@@ -1428,7 +1428,7 @@ func TestSyncConfigContext(t *testing.T) {
 	// trip schema header
 	now := time.Now()
 	stores[0].GetMeta().StatusAddress = server.URL[7:]
-	synced, _ := tc.syncStoreConfig(tc.GetStores())
+	synced, _, _ := tc.syncStoreConfig(tc.GetStores())
 	re.False(synced)
 	re.Less(time.Since(now), clientTimeout*2)
 }
@@ -1450,15 +1450,17 @@ func TestStoreConfigSync(t *testing.T) {
 	re.Equal(uint64(144), tc.GetStoreConfig().GetRegionMaxSize())
 	re.NoError(failpoint.Enable("github.com/tikv/pd/server/cluster/mockFetchStoreConfigFromTiKV", `return("10MiB")`))
 	// switchRaftV2 will be true.
-	synced, switchRaftV2 := tc.syncStoreConfig(tc.GetStores())
+	synced, switchRaftV2, needPersist := tc.syncStoreConfig(tc.GetStores())
 	re.True(synced)
 	re.True(switchRaftV2)
+	re.True(needPersist)
 	re.EqualValues(512, tc.opt.GetMaxMovableHotPeerSize())
 	re.Equal(uint64(10), tc.GetStoreConfig().GetRegionMaxSize())
 	// switchRaftV2 will be false this time.
-	synced, switchRaftV2 = tc.syncStoreConfig(tc.GetStores())
+	synced, switchRaftV2, needPersist = tc.syncStoreConfig(tc.GetStores())
 	re.True(synced)
 	re.False(switchRaftV2)
+	re.False(needPersist)
 	re.Equal(uint64(10), tc.GetStoreConfig().GetRegionMaxSize())
 	re.NoError(opt.Persist(tc.GetStorage()))
 	re.NoError(failpoint.Disable("github.com/tikv/pd/server/cluster/mockFetchStoreConfigFromTiKV"))