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Measuring and improving the energy performance with considering emission constraints is an important issue for China’s energy conservation, pollutant emissions reduction and environment protection. This study utilizes several data envelopment analysis (DEA) based models to evaluate the total-factor energy and emission performance of China’s 30 regions within a joint production framework of considering desirable and undesirable outputs as well as separated energy and non-energy inputs. DEA window analysis is applied in this study to deal with cross-sectional and time-varying data, so as to measure the performance during the period of 2000–2009. Two treatments for undesirable outputs are combined with DEA models and the associated indicators for simplex energy performance and unified energy and emission performance measurement are proposed and compared. The evaluation results indicate …