diff --git a/src/metric-engine/src/config.rs b/src/metric-engine/src/config.rs
index 150885ed49..e342cd9d73 100644
--- a/src/metric-engine/src/config.rs
+++ b/src/metric-engine/src/config.rs
@@ -17,13 +17,14 @@ use std::time::Duration;
 use common_telemetry::warn;
 use serde::{Deserialize, Serialize};
 
-/// The default flush interval of the metadata region.  
+/// The default flush interval of the metadata region.
 pub(crate) const DEFAULT_FLUSH_METADATA_REGION_INTERVAL: Duration = Duration::from_secs(30);
 
 /// Configuration for the metric engine.
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq)]
 pub struct EngineConfig {
     /// Whether to use sparse primary key encoding.
+    #[serde(default = "EngineConfig::default_sparse_primary_key_encoding")]
     pub sparse_primary_key_encoding: bool,
     /// The flush interval of the metadata region.
     #[serde(
@@ -37,7 +38,7 @@ impl Default for EngineConfig {
     fn default() -> Self {
         Self {
             flush_metadata_region_interval: DEFAULT_FLUSH_METADATA_REGION_INTERVAL,
-            sparse_primary_key_encoding: true,
+            sparse_primary_key_encoding: Self::default_sparse_primary_key_encoding(),
         }
     }
 }
@@ -47,6 +48,10 @@ impl EngineConfig {
         DEFAULT_FLUSH_METADATA_REGION_INTERVAL
     }
 
+    fn default_sparse_primary_key_encoding() -> bool {
+        true
+    }
+
     /// Sanitizes the configuration.
     pub fn sanitize(&mut self) {
         if self.flush_metadata_region_interval.is_zero() {