To perfect the modern university system with Chinese characteristics requires to deepen university management system reform from the internal. Since the promulgation and implementation of National medium and long-term education reform and development plan outline (2010-2020), reform practice of our university management system has yielded fruitful results, but it is also facing new difficulties and problems. In order to accelerate the innovative development of the university management system which with modern university, universities should devote to doing in follow aspects, such as to perfecting the university internal leadership system, deepening the innovation of the university and its colleges management system, promoting the personnel and distribution system, following up the financial management systems and so on.