Abstract: The interaction between government, university and market (society) constitutes the operation mechanism of university governance system. To realize the modernization of university governance system, it is necessary to achieve the coordinated development of the three elements, the combination of external control and autonomy, so as to ensure sustainable development of university functions. The government functions have been changed and the reform of educational administration system has been deepened through the reform of "releasing, managing and serving". In terms of the internal relationship coordination of universities, it is necessary to adhere to the concept of "Party committee leading, principle taking responsibility, professors governing academic studies, democratic management". In terms of the relationship between university and market (society), it is necessary to promote more market (society) factors to participate in the process of university governance.