It is of great significance to improve Total Factor Energy Efficiency (TFEE) for China‘s energy saving, emission reduction and ecological protection. This paper focuses on the calculation and decomposition of TFEE of eight economic regions in China considering the effects of undesirable outputs. The TFEE values of the eight economic regions in China are calculated via the input-oriented radial CRS super-efficiency SBM model. In order to overcome the shortcomings of the traditional ML index, this paper firstly builds an improved ML index using MinDS function, then decomposes the TFEE values through Zofio decomposition analysis method, and then identifies the driving factors of TFEE via Tobit model, and finally clarifies the path of improving TFEE in the economic regions. The findings show that the TFEE values of the eight economic regions in China are basically higher in the southeast and lower in the northwest. The dominant factor affecting the TFEE values in the eight economic regions is industrial structure, followed by technological development level. The research conclusions of this paper can provide reference for the formulation of policies for energy conservation and ecological protection.