How to run typescript-eslint on .ts files and eslint on .js files in the same project in VSCode

You need to override the configuration to use separate parsers for js and ts files. you can configure .eslintrc.js as below

module.exports = {
    root: true,    
    extends: [
      'eslint:recommended'
    ],
    "overrides": [
      {
        "files": ["**/*.ts", "**/*.tsx"],
        "env": { "browser": true, "es6": true, "node": true },
        "extends": [
          "eslint:recommended",
          "plugin:@typescript-eslint/eslint-recommended",
          "plugin:@typescript-eslint/recommended"
        ],
        "globals": { "Atomics": "readonly", "SharedArrayBuffer": "readonly" },
        "parser": "@typescript-eslint/parser",
        "parserOptions": {
          "ecmaFeatures": { "jsx": true },
          "ecmaVersion": 2018,
          "sourceType": "module",
          "project": "./tsconfig.json"
        },
        "plugins": ["@typescript-eslint"],
        "rules": {
          "indent": ["error", 2, { "SwitchCase": 1 }],
          "linebreak-style": ["error", "unix"],
          "quotes": ["error", "single"],
          "comma-dangle": ["error", "always-multiline"],
          "@typescript-eslint/no-explicit-any": 0
        }
      }
    ]
  };

Sample Project is here