diff --git a/src/query/service/src/pipelines/processors/transforms/hash_join/runtime_filter/convert.rs b/src/query/service/src/pipelines/processors/transforms/hash_join/runtime_filter/convert.rs
index 90f2a8a7737fa..0e620c733afae 100644
--- a/src/query/service/src/pipelines/processors/transforms/hash_join/runtime_filter/convert.rs
+++ b/src/query/service/src/pipelines/processors/transforms/hash_join/runtime_filter/convert.rs
@@ -55,9 +55,37 @@ pub async fn build_runtime_filter_infos(
     max_threads: usize,
 ) -> Result<HashMap<usize, RuntimeFilterInfo>> {
     let total_build_rows = packet.build_rows;
-    let Some(packets) = packet.packets else {
+    let Some(mut packets) = packet.packets else {
         return Ok(HashMap::new());
     };
+
+    // If multiple filters target the same scan, keep only the one with lowest selectivity
+    // Selectivity = build_rows / build_table_rows (same as should_enable_runtime_filter)
+    // Key: scan_id, Value: (best_filter_id, lowest_selectivity)
+    let mut best_filter_per_scan: HashMap<usize, (usize, f64)> = HashMap::new();
+    for pkt in packets.values() {
+        let desc = runtime_filter_descs.get(&pkt.id).unwrap();
+        let selectivity = desc
+            .build_table_rows
+            .map(|rows| total_build_rows as f64 / rows as f64)
+            .unwrap_or(f64::MAX);
+        for (_, scan_id) in &desc.probe_targets {
+            best_filter_per_scan
+                .entry(*scan_id)
+                .and_modify(|e| {
+                    if selectivity < e.1 {
+                        *e = (pkt.id, selectivity);
+                    }
+                })
+                .or_insert((pkt.id, selectivity));
+        }
+    }
+
+    // Remove filters that are not the best for any scan
+    let best_ids: std::collections::HashSet<usize> =
+        best_filter_per_scan.values().map(|(id, _)| *id).collect();
+    packets.retain(|id, _| best_ids.contains(id));
+
     let mut filters: HashMap<usize, RuntimeFilterInfo> = HashMap::new();
 
     // Iterate over all runtime filter packets