diff --git a/mysqlcluster/syncer/mysql_cm.go b/mysqlcluster/syncer/mysql_cm.go
index a419f3b1..943be49b 100644
--- a/mysqlcluster/syncer/mysql_cm.go
+++ b/mysqlcluster/syncer/mysql_cm.go
@@ -81,7 +81,7 @@ func buildMysqlConf(c *mysqlcluster.MysqlCluster) (string, error) {
 		addKVConfigsToSection(sec, mysql57Configs)
 	}
 
-	addKVConfigsToSection(sec, mysqlSysConfigs, mysqlCommonConfigs, mysqlStaticConfigs, c.Spec.MysqlOpts.MysqlConf)
+	addKVConfigsToSection(sec, mysqlSysConfigs, mysqlCommonConfigs, mysqlStaticConfigs)
 
 	if c.Spec.MysqlOpts.InitTokuDB {
 		addKVConfigsToSection(sec, mysqlTokudbConfigs)
@@ -93,6 +93,12 @@ func buildMysqlConf(c *mysqlcluster.MysqlCluster) (string, error) {
 		}
 	}
 
+	for _, para := range c.Spec.MysqlOpts.MysqlConf {
+		if sec.HasKey(para) {
+			sec.Key(para).SetValue(c.Spec.MysqlOpts.MysqlConf[para])
+		}
+	}
+
 	data, err := writeConfigs(cfg)
 	if err != nil {
 		return "", err