In order to make the complex assessment system become more intelligent and efficient for the application and realization technology in real system, the enterprise alliance and its business reconfiguration model for complex application system are processed. The enterprise alliance with dynamic reconfiguration and part feature is established by constructing the information platform The system can realize the informationize in enterprise and between enterprise. The cooperation between enterprises can also be supported. The order assignment problem in the enterprise with directed graph model is presented. Simulation results show that the model and the algorithm are effective to the problem.