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Satisfactory results of IS project performance evaluation depend on the perfection of the project performance evaluation index system and the accuracy of the evaluation model. This paper analyzes the relationship between IS project performance and project organization, project characteristics and in it an IS project performance evaluation system is constructed. By improving the traditional fuzzy neural network (FNN) and introducing Levenberg-Marquart optimal algorithm into the network, we establish a new fuzzy neural network (NFNN). As a result, comparative analysis of it is found that the NFNN has less error and it is closer to reality.