Abstract: The integrated information system for the enterprise consists of many applied of information systems(IS). The functions of the system may be greater than the sum of functions of all subsystems because of synergy among subsystems. It is important to evaluate synergy properly in the-performance evaluation of the IS applications. This paper provides a frame to evaluate the performance of the IS applications and presents a methodology to evaluate the synergy. The methodology firstly establishes a data flow table among the IS applications by analyzing the functions of the applications. And secondly it estimates the elements of the synergy coefficient matrix based on the data flow table. Finally we discuss the properties of the synergy coefficient matrix.