To actively promote the deep collaboration and coordinated development between enterprises and universities and research institutes has great importance to building an innovative country. In this paper, on the foundation of the knowledge description of Industry-University-Research Collaborative Innovation, at first, the index system of performance comprehensive evaluation of IU-R collaborative innovation project is established, then the BP neural network model of performance comprehensive evaluation of I-U-R collaborative Innovation project is proposed, and the algorithm of this network model is designed. Theoretical analysis and experimental results show the feasibility and validity of this model. The research work supplies a new way for the performance evaluation of I-U-R collaborative innovation project.