As a governance tool, project system has been embedded in the field of higher education in China, and gradually solidified into a common means of university governance. Project system not only brings positive effects such as governance efficiency and governance effect, but also violates academic rationality and academic rules, resulting in certain contradictions between academic governance and project governance, including the contradiction between the certainty, accuracy, uncertainty and fuzziness of governance objectives, the specificity, fragmentation, flexibility and integrity of governance modes, and the contradiction between top-down and bottom-up of power operation. Thus, we should innovate the academic evaluation system and mechanism by strengthening the system construction, and promote the reform of project system. We should adjust and optimize the part of project governance that is not suitable for academic evaluation reform and that does not respect the law of academic development. Then we can not only give full play to the unique advantages and technical rationality of project governance, but also follow the internal logic and development law of academic governance and academic evaluation, so as to maintain a certain tension space between academic governance and project governance.