.
├── package.json
├── src
│   ├── index.ts
├── tsconfig.json
└── tt
    ├── a
    │   └── aa.ts
    └── b
        └── bb.ts

my tsconfig.json

{
  "$schema": "https://json.schemastore.org/tsconfig",
  "compilerOptions": {
    "isolatedModules": true,
    "resolveJsonModule": true,
    "allowSyntheticDefaultImports": true,
    "declaration": true,
    "declarationMap": false,
    "esModuleInterop": true,
    "module": "commonjs",
    "moduleResolution": "node",
    "pretty": true,
    "strict": true,
    "incremental": false,
    "target": "es2021",
    "baseUrl": ".",
    "lib": ["es2021"],
    "outDir": "./dist",
    "rootDir": ".",
    "skipLibCheck": true,
    "forceConsistentCasingInFileNames": true,
    "rootDirs": [
      "src",
      "tt/b",
      "tt/a"
    ]
  },
  "include": ["src", "__tests__/**/*.ts", "tt"],
  "exclude": ["node_modules"]
}

// src/index.ts
import { b } from "./bb";
console.log(b);

// tt/a/aa.ts
export const a = 1;

// tt/b/bb.ts
import { a } from "./aa";
console.log(a);
export const b = 2;

while running tsup --watch

it errors

✘ [ERROR] Could not resolve "./bb"

    src/index.ts:1:18:
      1 │ import { b } from "./bb";
        ╵                   ~~~~~~

ESM Build failed
Error: Build failed with 1 error:
src/index.ts:1:18: ERROR: Could not resolve "./bb"
    at failureErrorWithLog (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:1575:15)
    at /Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:1033:28
    at runOnEndCallbacks (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:1447:61)
    at buildResponseToResult (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:1031:7)
    at /Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:1143:14
    at responseCallbacks.<computed> (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:680:9)
    at handleIncomingPacket (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:735:9)
    at Socket.readFromStdout (/Users/silentlee/Desktop/eslint-config-bnc/node_modules/.pnpm/[email protected]/node_modules/esbuild/lib/main.js:656:7)
    at Socket.emit (node:events:527:28)
    at addChunk (node:internal/streams/readable:315:12)
✘ [ERROR] Could not resolve "./bb"

    src/index.ts:1:18:
      1 │ import { b } from "./bb";
        ╵                   ~~~~~~

CJS Build failed

with ./node_modules/.bin/tsc --traceResolution | grep -A 41 "======== Resolving module './bb'" --color=auto

======== Resolving module './bb' from '/Users/silentlee/Desktop/eslint-config-bnc/src/index.ts'. ========
Explicitly specified module resolution kind: 'NodeJs'.
'rootDirs' option is set, using it to resolve relative module name './bb'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/src/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/src/bb' - 'true'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/src/bb' - 'false'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/src/bb' - 'false'.
Longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/src/bb' is '/Users/silentlee/Desktop/eslint-config-bnc/src/'.
Loading 'bb' from the root dir '/Users/silentlee/Desktop/eslint-config-bnc/src/', candidate location '/Users/silentlee/Desktop/eslint-config-bnc/src/bb'.
Loading module as file / folder, candidate module location '/Users/silentlee/Desktop/eslint-config-bnc/src/bb', target file type 'TypeScript'.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/bb.ts' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/bb.tsx' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/bb.d.ts' does not exist.
Directory '/Users/silentlee/Desktop/eslint-config-bnc/src/bb' does not exist, skipping all lookups in it.
Trying other entries in 'rootDirs'.
Loading 'bb' from the root dir '/Users/silentlee/Desktop/eslint-config-bnc/tt/b', candidate location '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/bb'.
Loading module as file / folder, candidate module location '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/bb', target file type 'TypeScript'.
File '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/bb.ts' exist - use it as a name resolution result.
======== Module name './bb' was successfully resolved to '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/bb.ts'. ========
======== Resolving module './aa' from '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/bb.ts'. ========
Explicitly specified module resolution kind: 'NodeJs'.
'rootDirs' option is set, using it to resolve relative module name './aa'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/src/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa' - 'false'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa' - 'true'.
Checking if '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/' is the longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa' - 'false'.
Longest matching prefix for '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa' is '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/'.
Loading 'aa' from the root dir '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/', candidate location '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa'.
Loading module as file / folder, candidate module location '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa', target file type 'TypeScript'.
File '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa.ts' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa.tsx' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa.d.ts' does not exist.
Directory '/Users/silentlee/Desktop/eslint-config-bnc/tt/b/aa' does not exist, skipping all lookups in it.
Trying other entries in 'rootDirs'.
Loading 'aa' from the root dir '/Users/silentlee/Desktop/eslint-config-bnc/src', candidate location '/Users/silentlee/Desktop/eslint-config-bnc/src/aa'.
Loading module as file / folder, candidate module location '/Users/silentlee/Desktop/eslint-config-bnc/src/aa', target file type 'TypeScript'.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/aa.ts' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/aa.tsx' does not exist.
File '/Users/silentlee/Desktop/eslint-config-bnc/src/aa.d.ts' does not exist.
Directory '/Users/silentlee/Desktop/eslint-config-bnc/src/aa' does not exist, skipping all lookups in it.
Loading 'aa' from the root dir '/Users/silentlee/Desktop/eslint-config-bnc/tt/a', candidate location '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/aa'.
Loading module as file / folder, candidate module location '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/aa', target file type 'TypeScript'.
File '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/aa.ts' exist - use it as a name resolution result.
======== Module name './aa' was successfully resolved to '/Users/silentlee/Desktop/eslint-config-bnc/tt/a/aa.ts'. ========

and it can build succeed with tsc