diff --git a/.changeset/hip-jars-boil.md b/.changeset/hip-jars-boil.md
new file mode 100644
index 0000000000..5bdbdf7c34
--- /dev/null
+++ b/.changeset/hip-jars-boil.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/calc-dep-state": major
+"pnpm": minor
+---
+
+**Semi-breaking.** Changed the location of unscoped packages in the virtual global store. They will now be stored under a directory named `@` to maintain a uniform 4-level directory depth.
diff --git a/packages/calc-dep-state/src/index.ts b/packages/calc-dep-state/src/index.ts
index f2b247a908..ad220305f4 100644
--- a/packages/calc-dep-state/src/index.ts
+++ b/packages/calc-dep-state/src/index.ts
@@ -107,8 +107,12 @@ export function * iterateHashedGraphNodes<T extends PkgMeta> (
       deps: _calcDepGraphHash(new Set(), depPath),
     }
     const hexDigest = hashObjectWithoutSorting(state, { encoding: 'hex' })
+    // Use @/ prefix for unscoped packages to maintain uniform 4-level directory depth
+    // Scoped: @scope/pkg/version/hash
+    // Unscoped: @/pkg/version/hash
+    const prefix = name.startsWith('@') ? '' : '@/'
     yield {
-      hash: `${name}/${version}/${hexDigest}`,
+      hash: `${prefix}${name}/${version}/${hexDigest}`,
       pkgMeta,
     }
   }