As an essential material basis and power source for economic and social development, Western China’s low energy use efficiency has hindered its sustainable economic development. This study aims to evaluate the total factor energy efficiency of the region and identify its influencing factors. A three-stage DEA model was used to measure the efficiency of 11 provinces from 2006 to 2021, and the Tobit model was employed to investigate internal factors. The findings show that (i) external environmental factors and stochastic perturbations have a significant impact on TFEE in the western region, overestimating integrated efficiency and scale efficiency and underestimating pure technical efficiency. (ii) the study of external influencing factors finds that the level of economic development increases input redundancy; the industrial structure increases capital input and labor input redundancy while decreasing energy input redundancy; and the energy consumption structure increases capital input and energy input redundancy while decreasing labor input redundancy. (iii) the study of internal influencing factors finds that the level of scientific and technological innovation, the level of openness to the outside world, and the TFEE have a positive correlation. In contrast, the intensity of environmental regulation has a negative correlation.