Abstract: The objectives of this paper are to measure China's total factor energy efficiencies under environmental constraints at city-level, and study the structure and causes of the inter-city differences of the efficiency. The methods of undesirable output SBM model, Theil index, and Theil index decomposition are adopted, and panel data of 102 typical resource-based cities in China from 2004 to 2012 are used in this paper. The results and conclusions are as follows. Firstly, most resource-based cities in China, except for 12 cities including Tangshan, are inefficient in total factor energies. There exist apparent differences in total factor energy efficiencies among the resource-based cities. Dividing all the resource-based cities into different groups based on region, comprehensive classification, and resource type, the average total factor energy efficiencies of resource-based cities within each group is calculated. It finds that there exist apparent differences among city groups. The Theil index of 102 typical resource-based cities during 2004-2012 shows that the difference among groups has not been narrowed. Secondly, when grouping the cities by region, the result of Theil index decomposition shows that the inner-group difference of each region is the major cause of the total energy efficiency difference (from 94.33% to 81.79%), and the inter-group difference is an increasingly important cause of the total energy efficiency difference (from 5.67% to 18.21%). In addition, the total energy efficiency difference of cities in the central region is the most important cause of the total energy efficiency difference (28.44% in 2012). Thirdly, when grouping the cities by comprehensive classification the result of Theil index decomposition shows that the inner-group difference of each class is the major cause of the total energy efficiency difference (from 89.69% to 86.90%), and the inter-group difference is the minor cause of the total energy efficiency difference (from 10.31% to 13.10%). In addition, the total energy efficiency difference in the group of mature cities is the most important cause of the total energy efficiency difference (56.79% in 2012). Fourthly, when grouping the cities by resource type, the result of Theil index decomposition shows that the inner-group difference of each resource type is the major cause of the total energy efficiency difference (from 80.91% to 84.23%), and the inter-group difference is the minor cause of the total energy efficiency difference (from 19.09% to 15.77%). In addition, the total energy efficiency difference of coal resource city group (41.31% in 2012) and comprehensive resource city group (22.38% in 2012) are the two most important causes of the total energy efficiency difference. Furthermore, the total energy efficiency difference of oil and gas resource city group was completely eliminated in 2012. The related implications are discussed based on the results of the empirical study.