This article summarises 15 factors that affect the collaborative innovation of industry, university and research through literature research and establishes the innovation entity and innovation environment subsystem of the collaborative innovation system of colleges and universities based on the theory of synergy. By setting system boundaries and causal relationship analysis, the dynamic model of the collaborative innovation system in colleges and universities is established, and the model's validity is verified. Combining the actual work, the enlightenment of collaborative innovation management in colleges and universities is as follows: Develop collaborative innovation led by scientific and technological talents strategy. Strengthen the policy and system support for collaborative innovation of colleges and universities. Improve the collaborative innovation input mechanism of institutions of higher learning.