diff --git a/python/sglang/srt/disaggregation/common/conn.py b/python/sglang/srt/disaggregation/common/conn.py
index 1a66c83ae0c9..f0856bd48cc4 100644
--- a/python/sglang/srt/disaggregation/common/conn.py
+++ b/python/sglang/srt/disaggregation/common/conn.py
@@ -337,6 +337,11 @@ def __init__(
         # FIXME: alias here: target_dp_group -> prefill_dp_rank
         self.target_dp_group = self.prefill_dp_rank
 
+        if self.prefill_pp_size == self.kv_mgr.pp_size:
+            self.target_pp_ranks = [self.kv_mgr.pp_rank]
+        else:
+            self.target_pp_ranks = [rank for rank in range(self.prefill_pp_size)]
+
         self.kv_mgr.required_prefill_response_num_table[self.bootstrap_room] = (
             self.required_prefill_response_num
         )
@@ -348,7 +353,7 @@ def __init__(
         if bootstrap_key not in self.kv_mgr.connection_pool:
             bootstrap_infos = []
             for target_tp_rank in self.target_tp_ranks:
-                for target_pp_rank in range(self.prefill_pp_size):
+                for target_pp_rank in reversed(self.target_pp_ranks):
                     bootstrap_info = self._get_bootstrap_info_from_server(
                         target_tp_rank, self.target_dp_group, target_pp_rank
                     )
@@ -605,4 +610,4 @@ def close(self):
             self.thread.join(timeout=2)
             logger.info("Server thread stopped")
 
-    def poll(self) -> KVPoll: ...
+    def poll(self) -> KVPoll: ...
\ No newline at end of file
diff --git a/python/sglang/srt/disaggregation/prefill.py b/python/sglang/srt/disaggregation/prefill.py
index e2a51e712f32..6c3c9fd46c59 100644
--- a/python/sglang/srt/disaggregation/prefill.py
+++ b/python/sglang/srt/disaggregation/prefill.py
@@ -1,3 +1,4 @@
+
 """
 Life cycle of a request in the prefill server
 
@@ -581,22 +582,37 @@ def get_transferred_rids(self: Scheduler) -> List[str]:
         return transferred_rids
 
     def process_prefill_chunk(self: Scheduler) -> None:
-        if self.last_batch and self.last_batch.forward_mode.is_extend():
-            if self.chunked_req:
-                # Move the chunked request out of the batch so that we can merge
-                # only finished requests to running_batch.
-                self.last_batch.filter_batch(chunked_req_to_exclude=self.chunked_req)
-                self.tree_cache.cache_unfinished_req(self.chunked_req, chunked=True)
-                if self.enable_overlap:
-                    # Delay KV transfer to process_batch_result_disagg_prefill when overlap is enabled to ensure results are resolved
-                    self.chunked_req.tmp_end_idx = min(
-                        len(self.chunked_req.fill_ids),
-                        len(self.chunked_req.origin_input_ids),
-                    )
-                else:
-                    self.send_kv_chunk(self.chunked_req)
-                # chunked request keeps its rid but will get a new req_pool_idx
+        chunked_req_to_exclude = set()
+        if self.chunked_req:
+            chunked_req_to_exclude.add(self.chunked_req)
+            self.tree_cache.cache_unfinished_req(self.chunked_req, chunked=True)
+            if self.enable_overlap:
+                # Delay KV transfer to process_batch_result_disagg_prefill when overlap is enabled to ensure results are resolved
+                self.chunked_req.tmp_end_idx = min(
+                    len(self.chunked_req.fill_ids),
+                    len(self.chunked_req.origin_input_ids),
+                )
+            else:
+                self.send_kv_chunk(self.chunked_req)
+            # chunked request keeps its rid but will get a new req_pool_idx
+            if self.tp_worker.model_runner.mambaish_config is not None:
+                self.req_to_token_pool.free(
+                    self.chunked_req.req_pool_idx, free_mamba_cache=False
+                )
+            else:
                 self.req_to_token_pool.free(self.chunked_req.req_pool_idx)
+            self.running_batch.batch_is_full = False
+        if self.last_batch and self.last_batch.forward_mode.is_extend():
+            if self.last_batch.chunked_req:
+                # In the context pipeline parallelism, after the last chunk, the current microbatch still track outdated chunked_req.
+                # We need to discard it.
+                chunked_req_to_exclude.add(self.last_batch.chunked_req)
+
+            last_bs = self.last_batch.batch_size()
+            self.last_batch.filter_batch(
+                chunked_req_to_exclude=list(chunked_req_to_exclude)
+            )
+            if self.last_batch.batch_size() < last_bs:
                 self.running_batch.batch_is_full = False
 
     def send_kv_chunk(