The system is very important to the modern university since it has functions of guarantee and promotion. Hence the modern university should attach importance to the system construction. The construction of the modern university connects closely with both its external relationships and the system construction of internal management. The former has a great impact on the development of modern university and the latter can provide the modern university an efficient development. The impact from the external relationships mainly embodies in the modern university’s relationships with government at all levels, enterprise, public institution, and other universities while the efficient development mainly reflects in three aspects: the operating system of administration, the academic power system and allocation incentive system. This article will give a comprehensive analysis of problems exist in Chinese universities’ governance structure system from a perspective of organization system designing. It will also give some countermeasures and proposals to improve the university’s governance structure and system construction based on the successful experience cases in Europe and the United States.