The construction of think tanks in universities not only expands the functions of universities, but also has a profound impact on the organization and culture of universities. To build a think tank, universities must clarify its connotation, characteristics and functions, emphasize its academic attributes, and commit to providing original and implementable policy analysis and suggestions. The construction of think tanks in universities and the development of universities must contrast and complement each other and bring out the best in each other.University-affiliated think tanks should be conducive to enhancing the comparative advantages of universities, to reforming the talent cultivation mode, and to the development of teachers and the integration of disciplines. They should focus on promoting the transformation of knowledge production mode in universities, pay attention to knowledge mobilization, highlighting the “purposefulness” of knowledge production. Therefore, the think tanks should be closely combined with the comprehensive reform of universities. However, university-affiliated think tanks also face ethical challenges, such as the collusion of power and knowledge, and the economism of academic research, which will erode the independence of universities to some extent and bring about cultural conflicts within universities. Therefore, universities must be more flexible to adapt to these changes.