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In this paper, 40 important factors which inflected the practicing of evaluation information systems was found, that was an obstacle to promote the evaluation software in China today. A four-layer complex system about problems in performance evaluation is created, which involves some tough problems existing in the process of performance evaluation and its information systems in China. Taking the management problems as orientation, the paper emphasizes particularly on the integrity and systemic of the problems existing in performance evaluation. The paper shows how to analysis multi-factors of evaluation with complex interpretive structural modeling systems (CISMS) and gives the computer arithmetic for multilevel system hierarchy. Forth more, the paper also shows a new methodology to analyze the requirements of evaluation software systems. Also a fishbone diagram of the software requirements of Chinese local government evaluation information systems is created by CISMS methods.