Energy is the material basis for social development and is closely related with the economy. Energy shortage, a low utilization rate of energy and the deterioration of the environment have become the main restrictions of economic development in China. Therefore, studying energy efficiency has a practical significance for developing a harmonious and sustainable energy economy and building a conservation-minded and harmonious society. Here, based on the three-stage DEA model we analyzed the energy efficiency of 29 provinces in China in 2009, set up an evaluation index system of energy efficiency to compare differences in energy efficiency among regions and provide regions with theoretical guidance to adjust energy consumption strategy and improve energy efficiency. We divided technical efficiency into pure technical efficiency and scale efficiency, analyzed energy efficiency with its numerical value and added environment variables to perfect the results. We found that scale efficiency is overestimated before eliminating external factors and environment variables and pure technical efficiency is underestimated. To solve this problem, regions should expand the scale of the enterprises and pay more attention to energy efficiency. The scale returns of most provinces in the third stage are increasing (except Shandong province), which shows that many enterprises are too small to reflect the economy scale. Therefore, all regions except Shandong should increase their energy inputs to obtain the economy scale of energy utilization. From a regional perspective, eastern energy efficiency is highest and western is the lowest. All regions should increase the size of enterprises to realize the scale economy. Central and western regions in China should strengthen mutual cooperation, bring into play their respective advantages, exploit new energy and new technology and improve the utilization ratio of energy.