This paper uses DEA model to analyze the total factor energy economy efficiency of 30 provinces, municipalities, and autonomous regions in China using data from 2000 to 2012. The results indicate that the average efficiency of the overall majority of provinces in China maintains a downward trend during the research period and low efficiency regions, especially Midwest regions, increase sharply. The reasons lie in carbon emissions and energy consumption structure, because they are the important influential factors of energy economy efficiency and regional differences. Based on threshold regression method, the paper makes China be divided into five groups: the low emissions and more reasonable group, the low emissions and less reasonable group, the high emissions and more reasonable group, the high emissions and less reasonable group, and the high emissions and unreasonable group. Then, on the basis of regional development characteristics, it makes suggestions on low-carbon green development according to circumstance and energy economy efficiency improvement from the perspective of demand and supply.