Abstract: With the progress of society, energy is closely related to the economic development and ecological environment issues. In this paper, the energy economy complex model is constructed based on ecological theory, which includes the concept of the sustainable theory and recycling economy, and then does an empirical study on the coordination of complex systems of China’s energy economy from 1987 to 2006. The results show that there are volatility and regression in the environmental protection during China’s energy economy complex system towards ordering process, which provides a reliable basis for the follow-up policy-making.