Abstract: In order to understand the causal relationship between knowledge collaboration and alliance enterprise innovation performance, a dynamic model of alliance enterprise innovation performance system is constructed and analyzed based on knowledge collaboration. The results show that the system dynamics model constructed by the institute is effective, and the simulation results can better simulate the actual situation of the innovation performance of the alliance enterprise based on knowledge collaboration; for the alliance enterprises, the knowledge collaboration has a good promotion effect on its innovation performance; and among the three factors of knowledge collaboration, namely knowledge activity collaboration, knowledge reciprocal collaboration and exchange study, are important to promote the innovation performance of alliance enterprises. However, due to the influence of internal and external factors, the effect of knowledge collaboration on the innovation performance of alliance enterprises is not immediately apparent, but with the increase of alliance time, the rate of improvement of corporate innovation performance is gradually rising.