diff --git a/br/pkg/lightning/restore/restore.go b/br/pkg/lightning/restore/restore.go
index 69b213c368..7ea7be3c9d 100644
--- a/br/pkg/lightning/restore/restore.go
+++ b/br/pkg/lightning/restore/restore.go
@@ -770,7 +770,12 @@ func (rc *Controller) restoreSchema(ctx context.Context) error {
 
 	go rc.listenCheckpointUpdates()
 
-	rc.sysVars = ObtainImportantVariables(ctx, rc.tidbGlue.GetSQLExecutor(), !rc.isTiDBBackend())
+	sysVars := ObtainImportantVariables(ctx, rc.tidbGlue.GetSQLExecutor(), !rc.isTiDBBackend())
+	// override by manually set vars
+	for k, v := range rc.cfg.TiDB.Vars {
+		sysVars[k] = v
+	}
+	rc.sysVars = sysVars
 
 	// Estimate the number of chunks for progress reporting
 	err = rc.estimateChunkCountIntoMetrics(ctx)
diff --git a/br/pkg/lightning/restore/restore_test.go b/br/pkg/lightning/restore/restore_test.go
index bbd23cbd71..fc44917fdf 100644
--- a/br/pkg/lightning/restore/restore_test.go
+++ b/br/pkg/lightning/restore/restore_test.go
@@ -1553,8 +1553,23 @@ func (s *restoreSchemaSuite) TearDownTest(c *C) {
 }
 
 func (s *restoreSchemaSuite) TestRestoreSchemaSuccessful(c *C) {
+	// before restore, if sysVars is initialized by other test, the time_zone should be default value
+	if len(s.rc.sysVars) > 0 {
+		tz, ok := s.rc.sysVars["time_zone"]
+		c.Assert(ok, IsTrue)
+		c.Assert(tz, Equals, "SYSTEM")
+	}
+
+	s.rc.cfg.TiDB.Vars = map[string]string{
+		"time_zone": "UTC",
+	}
 	err := s.rc.restoreSchema(s.ctx)
 	c.Assert(err, IsNil)
+
+	// test after restore schema, sysVars has been updated
+	tz, ok := s.rc.sysVars["time_zone"]
+	c.Assert(ok, IsTrue)
+	c.Assert(tz, Equals, "UTC")
 }
 
 func (s *restoreSchemaSuite) TestRestoreSchemaFailed(c *C) {
diff --git a/br/pkg/lightning/restore/tidb.go b/br/pkg/lightning/restore/tidb.go
index 31639ffdfd..680cd1558e 100644
--- a/br/pkg/lightning/restore/tidb.go
+++ b/br/pkg/lightning/restore/tidb.go
@@ -83,7 +83,6 @@ func isUnknownSystemVariableErr(err error) bool {
 }
 
 func DBFromConfig(ctx context.Context, dsn config.DBStore) (*sql.DB, error) {
-
 	param := common.MySQLConnectParam{
 		Host:             dsn.Host,
 		Port:             dsn.Port,