In order to realize the connotative development of higher education and deepen the comprehensive reform of education in e new era,it is urgent to innovate the modern university system. Through taking the following steps,i. e. meeting the needs of the re- rm and development of higher education in modern China,adhering to the spirit of modern universities,and improving the governance ructure of modern universities,we can coordinate the new internal and external relations of interests and resource allocation of all par- es,improve the internal management system and operation mechanism of modern colleges and universities,and solve the dilemma of novating the modern university system based on the separation of government and school and the separation of management and man- gement,and then improving the new modern university system with Chinese characteristics for the purpose of clarifying the autonomy f running schools,the right to academic freedom and the improvement of leadership. Besides,only in that way can colleges and uni- ersities effectively accelerate the pace of“double first - class”construction and achieve the goal of rapidly connotative development of niversity in China.