The invention discloses a centralized configuration and remote deployment method for a Java Web application. According to the method, a server, a Java application middleware and an application system are registered, configured, deployed and controlled by means of management services operating independently, server operation data, middleware operation data and application system operation data are received and stored, and the data are analyzed; the Java application middleware of a computer is configured and controlled through a distributed Agent program, and meanwhile the operation data of the server and the operation data of the Java application middleware are collected; the operation data, including a memory, a thread, stack, class loading and the like, of the Java application middleware are collected by means of a plug-in technology, and the data are collected and gathered to the management services through an Agent in an asynchronous mode. According to the method, by means of the Agent, the operation data collection capacity and the application deployment and control capacity in a cluster environment are provided, the monitoring capacity unrelated to an appliance system is provided in a middleware extension plug-in mode, and the non-invasive collection problem of the operation data of the server, the application middleware and the application system in the large-scale cluster environment is effectively solved.