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Good software architecture can provide reliable stability and scalability for application systems and simplify the implementation process of application systems. In view of the application system based on the Java EE platform, a Java EE application architecture which based on ESMSH framework is proposed. The architecture is based on MVC design patter,it uses the Easy UI to build the presentation layer, uses the Spring MVC framework to build the control layer, and uses the JSON format to transmit data at the presentation layer and the control layer. using the Spring framework to build the business logic layer, using the Hibernate framework to build the data persistence layer, the components dependencies of the control layer, business layer, and data persistence layer is managed through the IOC container,the method of annotations is used for the architecture’s integration and development. The architecture is applied to the implementation of the target management system of colleges and universities, According to Java EE layered development method for system design, and the implementation process of each layer is described in detail.The effectiveness of the architecture is proved through practice.