Purpose - The industrial structure upgrading can play an important role in promoting the carbon emission efficiency. Thus, this paper attempts to study the impact of industrial structure upgrading on carbon emission efficiency in order to reduce carbon emissions. Research design, data, and methodology - This paper selects panel data of 30 provinces and municipalities (autonomous regions) in China from 2001 to 2016, and divides them into three regions. The Moore index is used to measure the industrial structure upgrading, the non-radial SBM model based on undesired output is used to measure the slack variable to calculate the total factor carbon emission efficiency. Finally the impact of industrial structure upgrading on the carbon emission efficiency are analyzed. Results - It is found that the Moore index and the carbon emission efficiency in the eastern region is the highest in the three regions. Conclusions - The influence of various influencing factors on carbon emission efficiency is different between regions. The Moore index has a positive effect on the carbon emission efficiency in the eastern region, and has a negative influence coefficient on the central region. The effect on the western region is not obvious.