Abstract: We seek to establish a complete system of ecological civilization system, from the concept innovation,the top design innovation, the management system innovation and the mechanism innovation dimensions,only to make the whole system based on theoretical foundation, top-level design guidance, management system support,and dynamic driven mechanism form a self-organization system. “Imitating nature” and other traditional philosophical ideas can consolidate the theoretical basis of the concept of ecological civilization. The top-level design innovation focuses on the systematic, holistic and collaborative nature in “five one” internal reform of the whole system. Innovation of management system involves the three interrelated links, namely to determine the ecological scale,distribution of property rights and market transaction. Dynamic mechanism innovation includes the relative equilibrium configuration benefit mechanism and the social supervision mechanism.