Abstract:The university-industry research deep integration is a key link in the series of deployments to improve China's science and technology innovation system mechanism, but the existing research does not reflect the dynamic, stage and multi-subject characteristics of the deep integration process. In view of this, the idea of the innovation process stages was introduced into the establishment of the mechanism of U-I relations, and a multi-stage evolutionary game model of U-IR deep integration among the local government, enterprises, universities, research institutions, financial institutions, science and technology intermediary, and users was contracted. Based on the three-party evolutionary game theory, the strategy selection of the participants in different stages during the U-IR deep integration process was further analyzed using the Jacobian matrix and Lyapunov’s indirect method. The influence of key factors on the evolution of each party’s strategy in different situations was studied by simulation using Matlab software. The main results show that both financial support and policy support by the local governments are conducive to the IUR deep integration, but, excessive financial support may lead to speculation, thereby weakening the guiding effect of the government. Reasonable punishment mechanisms can enhance the willingness of innovation subjects to continue to participate in deep integration. Compared with the average distribution mechanism and the cost-based distribution mechanism, the revenue allocation based on relative risk sharing can make the profits obtained by all innovation subjects more closely match the risk undertaken, to enhance the willingness of innovation subjects to participate in IUR deep Integration. Since integration can effectively absorb the uncertainty risks in the innovation process and realize risk sharing, the integration subject will tend to deeply integrate. Finally, relevant suggestions are made for the construction of the U-IR deep integration mechanism.