diff --git a/tests/framework/e2e/cluster.go b/tests/framework/e2e/cluster.go
index 3da0ff9a8f2..ddcc4578b3b 100644
--- a/tests/framework/e2e/cluster.go
+++ b/tests/framework/e2e/cluster.go
@@ -32,6 +32,7 @@ import (
 	"go.uber.org/zap/zaptest"
 
 	"go.etcd.io/etcd/api/v3/etcdserverpb"
+	"go.etcd.io/etcd/api/v3/version"
 	clientv3 "go.etcd.io/etcd/client/v3"
 	"go.etcd.io/etcd/pkg/v3/featuregate"
 	"go.etcd.io/etcd/pkg/v3/proxy"
@@ -630,6 +631,10 @@ func (cfg *EtcdProcessClusterConfig) EtcdServerProcessConfig(tb testing.TB, i in
 	default:
 		panic(fmt.Sprintf("Unknown cluster version %v", cfg.Version))
 	}
+	v, err := GetVersionFromBinary(execPath)
+	if err != nil {
+		panic(err)
+	}
 
 	defaultValues := values(*embed.NewConfig())
 	overrideValues := values(cfg.ServerConfig)
@@ -640,6 +645,12 @@ func (cfg *EtcdProcessClusterConfig) EtcdServerProcessConfig(tb testing.TB, i in
 		if flag == "experimental-snapshot-catchup-entries" && !CouldSetSnapshotCatchupEntries(execPath) {
 			continue
 		}
+		if flag == "experimental-compaction-batch-limit" {
+			continue
+		}
+		if flag == "compaction-batch-limit" && v.LessThan(version.V3_6) {
+			flag = "experimental-compaction-batch-limit"
+		}
 		args = append(args, fmt.Sprintf("--%s=%s", flag, value))
 	}
 	envVars := map[string]string{}