Objectively evaluating the efficiency of input and output of the energy in Chongqing, exploiting the relationship between environment pollution, energy consumption and economic growth, and optimizing the energy structure, are the important issues for guiding energy consumption of Chongqing to the direction of green and low carbon and the important basis of policy-making for energy saving and pollution reduction, and strategy-making of energy development and economic planning. In this work, we scientifically grouped the energy input and economic and social output factors, and then used data envelopment analysis (DEA) to construct an energy demand structure equation and a DEA model. And a series of DEA empirical studies on energy consumption in Chongqing were conducted. The variation of scale efficiency of Chongqing energy input and output in different historical periods and different stages, the energy redundant input value (radial improvement and relaxation improvement), the scale effect value, the comprehensive technical efficiency value and the pure technical efficiency value were obtained, and then the effective production frontiers of DEA weak efficiency, DEA efficiency and DEA complete efficiency were determined. Based on these results, the energy structure from 2016 to 2020 in Chongqing was optimized. The research results can provide a scientific basis for the green and low carbon development of Chongqing and optimizing the its energy consumption structure in the 13th Five-Year Plan.