According to this post and this post, I can install packages by using command
npm install --prefix <path/to/prefix_folder> -g
--prefix is for specifying the location and -g is tell the npm to globally install. 
However, neither using -g nor doesn't, it entirely copies my project to the prefix folder and create an npm_modules in the root of the cloned project while I execute the command!! Without --prefix the command can install packages correctly. 
the package.json as bellow:
{
  "name": "Javims-cms",
  "version": "1.0.0",
  "scripts": {
    "start": "concurrently \"npm run tsc:w\" \"npm run lite\" ",    
    "tsc": "tsc -p D:/localhost.server.com/projects/javims/mysite/cms",
    "tsc:w": "tsc -w -p D:/localhost.server.com/projects/javims/mysite/cms",
    "lite": "lite-server",
    "typings": "typings",
    "postinstall": "typings install" 
  },
  "license": "ISC",
  "dependencies": {
    "angular2": "2.0.0-beta.7",
    "systemjs": "0.19.22",
    "es6-promise": "^3.0.2",
    "es6-shim": "^0.33.3",
    "reflect-metadata": "0.1.2",
    "rxjs": "5.0.0-beta.2",
    "zone.js": "0.5.15",
  },
  "devDependencies": {
    "concurrently": "^2.0.0",
    "lite-server": "^2.1.0",
    "typescript": "^1.8.2",
    "typings":"^0.6.8"
  }
}
Updates:
//the file structure of my project:  
myproject(project root)
    -access
    -package.json
    -typings.json
    -tsconfig.json
//the file structure after I run npm install --prefix ./access [-g] from project root
myproject(project root)
      -access
         -npm_modules
              -myproject(project root)
              -access
                 -npm_modules
                     - [packages]
              -package.json
              -typings.json
              -tsconfig.json
      -package.json
      -typings.json
      -tsconfig.json
//what I am expecting
myproject(project root)
   -access
      -npm_modules
          -(packages)
   -package.json
   -typings.json
   -tsconfig.json
 
    