Abstract: Building a modern university system needs constant transform of the existing university system,which faces the value difference between university and government, universities and society, academic and administrative. More specifically,they are value difference between autonomy and controlled, transcendence and adaptation, freedom and order. Each value has its limitation and rationality, we cannot confirm one but negative the other one. Autonomy, transcendence and freedom are the substant values of the University.Therefore,we need innovate university system adjusting the relationship betwwen university and government, universities and society, academic and administrative, to achieve the balance between autonomy and controlled, transcendence and adaptation, the balance between freedom and order.The most important is that autonomy, transcendence and freedom should be focuses in the ballance.