Collaborative innovation platform is an effective carrier for gathering and integrating innovation resources, and knowledge flow has an important impact on the orderly operation of collaborative innovation platform. Therefore, it is necessary to carry out effective governance of the platform to guarantee the smooth flow of knowledge, so as to promote the sustainable development of the collaborative innovation platform. Based on this, the system dynamics model was used to analyze the impact of collaborative innovation platform governance mechanism on knowledge flow. First, the knowledge flow process of collaborative innovation platform was analyzed and the connotation of governance mechanism of collaborative innovation platform was clarified. Secondly, the impact of the governance mechanism of collaborative innovation platform on knowledge flow was analyzed, and then a theoretical model was constructed. Finally, system dynamics was applied to construct a system dynamics model of the influence of collaborative innovation platform governance mechanism on knowledge flow, and the model was simulated with by Vensim PLE to reveal the role of collaborative innovation platform governance mechanism on knowledge flow. The results show that both contract and relationship governance mechanisms have a positive impact on the knowledge flow of collaborative platforms, with the relational governance mechanism playing a stronger role, and the simultaneous use of both types of governance mechanisms is more conducive to the promotion of the knowledge flow of collaborative platforms. The results further show that the combination of strong contract and strong relationship governance mechanism can better promote the knowledge flow of collaborative platform under different degrees of knowledge failure and initial knowledge potential difference. It can provide references for the policy formulation and improvement of collaborative innovation platforms in China.