Pharmaceutical enterprise management system based on JavaEE can as work platform, enterprise management personnel in a timely manner to provide pharmaceutical companies operating in the process of all kinds of information, improve managers in the management of user efficiency and level of employment, with strong adaptability and practicability. Based on the JavaEE pharmaceutical enterprise management system design and implementation of this paper discusses the principle and structure of the system, proved that the optimal management system with flexible mechanism, high safety, easy to extend.