The invention discloses a method and a system for operating a JAVA 2 Enterprise Edition (J2EE)-based Web application system. Web application files with the same service functions are uniformly stored in advance to form service modules. The method comprises the following steps of: establishing a platform service end on a center application server, and performing centralized issue and management on the service modules; downloading the service modules from the platform service end on the center application server and installing the required service modules through an application server in a local area network; and supplying services to clients through the application server by using the installed service modules. The method and the system can reduce waste of stored resources of the enterprise-level Web application system in the operating process.