Abstract: The governance of university think tanks mainly relies on the three mechanisms of organization, system and value. The three mechanisms are interdependent and support each other in the process of university think tank governance. As the construction of Chinese university think tanks has begun to take shape, how to improve the connotation of university think tanks with quality as the core has gradually become a new challenge for university think tank construction. By analyzing the governance dilemmas faced by university think tanks on the three levels of organization, system and value, it is proposed that the organization, system and value mechanism of university think tanks should be adjusted, standardized and interacted with each other, so as to enhance the ability of the university think tank governance body and increase the cooperative consensus for university co-governance.