Energy is the material basis for urban economic development, which has an increasingly prominent constraint role to the urban ecological economic system (UEES). The research related to the theories and methods for sustainable use of energy in the UEES has been paid more attention. However, the current research about energy structure evolution in the system and the quantitative understanding of energy flow is not enough in depth. In this paper, the energy structure and the mechanism of energy flows in the UEES were systematically analyzed based on the theories of systematic and ecological economics, with taking Xiamen City in China as an example. Such studies are of important theoretical and practical significance for improving the structure and function of the UEES and achieving the ecological development of the system.