diff --git a/Cargo.lock b/Cargo.lock
index 5a56f6220c2b..573705ad4c48 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1823,7 +1823,7 @@ version = "0.2.0"
 dependencies = [
  "common-error",
  "pprof",
- "protobuf",
+ "prost",
  "snafu",
  "tokio",
 ]
@@ -6603,8 +6603,11 @@ dependencies = [
  "nix 0.26.2",
  "once_cell",
  "parking_lot 0.12.1",
+ "prost",
+ "prost-build",
+ "prost-derive",
  "protobuf",
- "protobuf-codegen-pure",
+ "sha2",
  "smallvec",
  "symbolic-demangle",
  "tempfile",
@@ -6888,16 +6891,6 @@ dependencies = [
  "protobuf",
 ]
 
-[[package]]
-name = "protobuf-codegen-pure"
-version = "2.28.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "95a29399fc94bcd3eeaa951c715f7bea69409b2445356b00519740bcd6ddd865"
-dependencies = [
- "protobuf",
- "protobuf-codegen",
-]
-
 [[package]]
 name = "ptr_meta"
 version = "0.1.4"
diff --git a/src/common/pprof/Cargo.toml b/src/common/pprof/Cargo.toml
index d5202974e598..0a29893097dc 100644
--- a/src/common/pprof/Cargo.toml
+++ b/src/common/pprof/Cargo.toml
@@ -8,9 +8,9 @@ license.workspace = true
 common-error = { path = "../error" }
 pprof = { version = "0.11.1", features = [
     "flamegraph",
-    "protobuf-codec",
+    "prost-codec",
     "protobuf",
 ] }
-protobuf = "2"
+prost.workspace = true
 snafu.workspace = true
 tokio.workspace = true
diff --git a/src/common/pprof/src/lib.rs b/src/common/pprof/src/lib.rs
index 62ccdd543faf..b6f1af477e92 100644
--- a/src/common/pprof/src/lib.rs
+++ b/src/common/pprof/src/lib.rs
@@ -16,7 +16,7 @@ use std::any::Any;
 use std::time::Duration;
 
 use common_error::prelude::{ErrorExt, StatusCode};
-use pprof::protos::Message;
+use prost::Message;
 use snafu::{ResultExt, Snafu};
 
 #[derive(Debug, Snafu)]
@@ -32,9 +32,6 @@ pub enum Error {
 
     #[snafu(display("Failed to create pprof report, source: {}", source))]
     ReportPprof { source: pprof::Error },
-
-    #[snafu(display("Failed to write report, source: {}", source))]
-    WriteReport { source: protobuf::ProtobufError },
 }
 
 pub type Result<T> = std::result::Result<T, Error>;
@@ -93,12 +90,10 @@ impl Profiling {
 
     /// Profiles and returns a generated proto.
     pub async fn dump_proto(&self) -> Result<Vec<u8>> {
-        let mut body: Vec<u8> = Vec::new();
-
         let report = self.report().await?;
         // Generate google’s pprof format report.
         let profile = report.pprof().context(ReportPprofSnafu)?;
-        profile.write_to_vec(&mut body).context(WriteReportSnafu)?;
+        let body = profile.encode_to_vec();
 
         Ok(body)
     }