diff --git a/embed/templates/scripts/run_drainer.sh.tpl b/embed/templates/scripts/run_drainer.sh.tpl
index ce8a76bafa..fcc1fb4012 100644
--- a/embed/templates/scripts/run_drainer.sh.tpl
+++ b/embed/templates/scripts/run_drainer.sh.tpl
@@ -29,5 +29,4 @@ exec bin/drainer \
     --pd-urls="{{template "PDList" .Endpoints}}" \
     --data-dir="{{.DataDir}}" \
     --log-file="{{.LogDir}}/drainer.log" \
-    --config=conf/drainer.toml \
-    --initial-commit-ts={{.CommitTs}} 2>> "{{.LogDir}}/drainer_stderr.log"
+    --config=conf/drainer.toml 2>> "{{.LogDir}}/drainer_stderr.log"
diff --git a/pkg/cluster/ansible/service.go b/pkg/cluster/ansible/service.go
index 7b98161516..b93b4a46a8 100644
--- a/pkg/cluster/ansible/service.go
+++ b/pkg/cluster/ansible/service.go
@@ -196,7 +196,8 @@ func parseDirs(ctx context.Context, user string, ins spec.InstanceSpec, sshTimeo
 			if strings.Contains(line, "--initial-commit-ts=") {
 				tsArg := strings.Split(line, " ")[4] // 4 whitespaces ahead
 				tmpTs, _ := strconv.Atoi(strings.TrimPrefix(tsArg, "--initial-commit-ts="))
-				newIns.CommitTS = int64(tmpTs)
+				newIns.Config = make(map[string]interface{})
+				newIns.Config["initial_commit_ts"] = int64(tmpTs)
 			}
 		}
 		return newIns, nil
diff --git a/pkg/cluster/spec/drainer.go b/pkg/cluster/spec/drainer.go
index 6066648108..80676d46c4 100644
--- a/pkg/cluster/spec/drainer.go
+++ b/pkg/cluster/spec/drainer.go
@@ -38,7 +38,7 @@ type DrainerSpec struct {
 	DeployDir       string                 `yaml:"deploy_dir,omitempty"`
 	DataDir         string                 `yaml:"data_dir,omitempty"`
 	LogDir          string                 `yaml:"log_dir,omitempty"`
-	CommitTS        int64                  `yaml:"commit_ts" default:"-1" validate:"commit_ts:editable"`
+	CommitTS        *int64                 `yaml:"commit_ts,omitempty" validate:"commit_ts:editable"` // do not use it anymore, exist for compatibility
 	Offline         bool                   `yaml:"offline,omitempty"`
 	NumaNode        string                 `yaml:"numa_node,omitempty" validate:"numa_node:editable"`
 	Config          map[string]interface{} `yaml:"config,omitempty" validate:"config:ignore"`
@@ -168,8 +168,6 @@ func (i *DrainerInstance) InitConfig(
 		paths.Log,
 	).WithPort(spec.Port).WithNumaNode(spec.NumaNode).AppendEndpoints(topo.Endpoints(deployUser)...)
 
-	cfg.WithCommitTs(spec.CommitTS)
-
 	fp := filepath.Join(paths.Cache, fmt.Sprintf("run_drainer_%s_%d.sh", i.GetHost(), i.GetPort()))
 
 	if err := cfg.ConfigToFile(fp); err != nil {
diff --git a/pkg/cluster/spec/spec.go b/pkg/cluster/spec/spec.go
index 4337efe188..f8b6370e87 100644
--- a/pkg/cluster/spec/spec.go
+++ b/pkg/cluster/spec/spec.go
@@ -356,6 +356,9 @@ func (s *Specification) UnmarshalYAML(unmarshal func(interface{}) error) error {
 		}
 	}
 
+	// --initial-commit-ts should not be recorded at run_drainer.sh #1682
+	s.removeCommitTS()
+
 	return s.Validate()
 }
 
@@ -866,6 +869,21 @@ func setHostArch(field reflect.Value, hostArch map[string]string) error {
 	return nil
 }
 
+// when upgrade form old tiup-cluster, replace spec.CommitTS with spec.Config["initial_commit_ts"]
+func (s *Specification) removeCommitTS() {
+	_, ok1 := s.ServerConfigs.Drainer["initial_commit_ts"]
+	for _, spec := range s.Drainers {
+		_, ok2 := spec.Config["initial_commit_ts"]
+		if !ok1 && !ok2 && spec.CommitTS != nil && *spec.CommitTS != -1 {
+			if spec.Config == nil {
+				spec.Config = make(map[string]interface{})
+			}
+			spec.Config["initial_commit_ts"] = *spec.CommitTS
+		}
+		spec.CommitTS = nil
+	}
+}
+
 // GetGrafanaConfig returns global grafana configurations
 func (s *Specification) GetGrafanaConfig() map[string]string {
 	return s.ServerConfigs.Grafana
diff --git a/pkg/cluster/template/scripts/drainer.go b/pkg/cluster/template/scripts/drainer.go
index ed2831965a..c1f0c1030e 100644
--- a/pkg/cluster/template/scripts/drainer.go
+++ b/pkg/cluster/template/scripts/drainer.go
@@ -31,7 +31,6 @@ type DrainerScript struct {
 	DataDir   string
 	LogDir    string
 	NumaNode  string
-	CommitTs  int64
 	Endpoints []*PDScript
 }
 
@@ -44,7 +43,6 @@ func NewDrainerScript(nodeID, ip, deployDir, dataDir, logDir string) *DrainerScr
 		DeployDir: deployDir,
 		DataDir:   dataDir,
 		LogDir:    logDir,
-		CommitTs:  -1,
 	}
 }
 
@@ -60,12 +58,6 @@ func (c *DrainerScript) WithNumaNode(numa string) *DrainerScript {
 	return c
 }
 
-// WithCommitTs set CommitTs field of DrainerScript
-func (c *DrainerScript) WithCommitTs(ts int64) *DrainerScript {
-	c.CommitTs = ts
-	return c
-}
-
 // AppendEndpoints add new DrainerScript to Endpoints field
 func (c *DrainerScript) AppendEndpoints(ends ...*PDScript) *DrainerScript {
 	c.Endpoints = append(c.Endpoints, ends...)