Cocos2d-js project structure is really simple to understand. so let's look at screenshoot of a folder with a Cocos2d-js project.

•  The frameworks  directory, its contains Cocos2d-html5 engine and the Cocos2d-x JavaScript Bindings and Runtime including iOS/MacOSX/Android/Linux/Windows platforms.
• The res  directory, resources folder of the project must save all images, audio, fonts, animations, etc.
• The runtime directory , its including all executables package under development.
• The src directory ,  The most important directory is src directory .Because your game business logic in written in there.
• index.html   The main web page of project.  You can access when you start web server .
• main.js  is the starter script  of project.contains initialization code
• project.json   Project configuration file, detailed information can be found in here.