diff --git a/.changeset/stale-bars-tan.md b/.changeset/stale-bars-tan.md
new file mode 100644
index 0000000000..5a8afca6ce
--- /dev/null
+++ b/.changeset/stale-bars-tan.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/dependency-path": patch
+"@pnpm/calc-dep-state": patch
+---
+
+Fix dependency graph hash calculation for runtime dependencies (like Node.js, Deno).
diff --git a/packages/calc-dep-state/src/index.ts b/packages/calc-dep-state/src/index.ts
index d9c790331e..f2b247a908 100644
--- a/packages/calc-dep-state/src/index.ts
+++ b/packages/calc-dep-state/src/index.ts
@@ -48,7 +48,15 @@ function calcDepGraphHash<T extends string> (
   if (cache[depPath]) return cache[depPath]
   const node = depsGraph[depPath]
   if (!node) return ''
-  node.fullPkgId ??= createFullPkgId(node.pkgIdWithPatchHash!, node.resolution!)
+  if (!node.fullPkgId) {
+    if (!node.pkgIdWithPatchHash) {
+      throw new Error(`pkgIdWithPatchHash is not defined for ${depPath} in depsGraph`)
+    }
+    if (!node.resolution) {
+      throw new Error(`resolution is not defined for ${depPath} in depsGraph`)
+    }
+    node.fullPkgId = createFullPkgId(node.pkgIdWithPatchHash, node.resolution)
+  }
   const deps: Record<string, string> = {}
   if (Object.keys(node.children).length && !parents.has(node.fullPkgId)) {
     const nextParents = new Set([...Array.from(parents), node.fullPkgId])
@@ -135,6 +143,6 @@ function lockfileDepsToGraphChildren (deps: Record<string, string>): Record<stri
 }
 
 function createFullPkgId (pkgIdWithPatchHash: PkgIdWithPatchHash, resolution: LockfileResolution): string {
-  const res = 'integrity' in resolution ? resolution.integrity : JSON.stringify(resolution)
+  const res = 'integrity' in resolution ? resolution.integrity : hashObject(resolution)
   return `${pkgIdWithPatchHash}:${res}`
 }
diff --git a/packages/dependency-path/src/index.ts b/packages/dependency-path/src/index.ts
index a0d409ca7a..d6e7c23d07 100644
--- a/packages/dependency-path/src/index.ts
+++ b/packages/dependency-path/src/index.ts
@@ -66,9 +66,6 @@ export function getPkgIdWithPatchHash (depPath: DepPath): PkgIdWithPatchHash {
   if (sepIndex !== -1) {
     pkgId = pkgId.substring(0, sepIndex)
   }
-  if (pkgId.includes(':')) {
-    pkgId = pkgId.substring(pkgId.indexOf('@', 1) + 1)
-  }
   return pkgId as PkgIdWithPatchHash
 }
 
diff --git a/packages/dependency-path/test/index.ts b/packages/dependency-path/test/index.ts
index d03b574a3b..73cb53219c 100644
--- a/packages/dependency-path/test/index.ts
+++ b/packages/dependency-path/test/index.ts
@@ -1,6 +1,7 @@
 /// <reference path="../../../__typings__/index.d.ts"/>
 import {
   depPathToFilename,
+  getPkgIdWithPatchHash,
   isAbsolute,
   parse,
   refToRelative,
@@ -109,3 +110,32 @@ test('tryGetPackageId', () => {
   expect(tryGetPackageId('/@(-.-)/foo@1.0.0(@types/babel__core@7.1.14)' as DepPath)).toEqual('/@(-.-)/foo@1.0.0')
   expect(tryGetPackageId('foo@1.0.0(patch_hash=xxxx)(@types/babel__core@7.1.14)' as DepPath)).toEqual('foo@1.0.0')
 })
+
+test('getPkgIdWithPatchHash', () => {
+  // Runtime dependency
+  expect(getPkgIdWithPatchHash('node@runtime:24.11.1' as DepPath)).toBe('node@runtime:24.11.1')
+
+  // Regular packages
+  expect(getPkgIdWithPatchHash('foo@1.0.0' as DepPath)).toBe('foo@1.0.0')
+
+  // Packages with patch hash
+  expect(getPkgIdWithPatchHash('foo@1.0.0(patch_hash=xxxx)' as DepPath)).toBe('foo@1.0.0(patch_hash=xxxx)')
+
+  // Packages with peer dependencies (should remove peer dependencies)
+  expect(getPkgIdWithPatchHash('foo@1.0.0(@types/babel__core@7.1.14)' as DepPath)).toBe('foo@1.0.0')
+
+  // Packages with both patch hash and peer dependencies (should keep patch hash, remove peer dependencies)
+  expect(getPkgIdWithPatchHash('foo@1.0.0(patch_hash=xxxx)(@types/babel__core@7.1.14)' as DepPath)).toBe('foo@1.0.0(patch_hash=xxxx)')
+
+  // Scoped packages
+  expect(getPkgIdWithPatchHash('@foo/bar@1.0.0' as DepPath)).toBe('@foo/bar@1.0.0')
+
+  // Scoped packages with patch hash
+  expect(getPkgIdWithPatchHash('@foo/bar@1.0.0(patch_hash=yyyy)' as DepPath)).toBe('@foo/bar@1.0.0(patch_hash=yyyy)')
+
+  // Scoped packages with peer dependencies
+  expect(getPkgIdWithPatchHash('@foo/bar@1.0.0(@types/node@18.0.0)' as DepPath)).toBe('@foo/bar@1.0.0')
+
+  // Scoped packages with both patch hash and peer dependencies
+  expect(getPkgIdWithPatchHash('@foo/bar@1.0.0(patch_hash=zzzz)(@types/node@18.0.0)' as DepPath)).toBe('@foo/bar@1.0.0(patch_hash=zzzz)')
+})