Abstract: In the new stage of historical development, there is an urgent need for low-carbon transformation in economic development. Energy conservation and emission reduction, green low carbon have become the top priorities of China's economic development. Improving carbon emission efficiency is the key to achieve the carbon peaking and carbon neutrality goals while maintaining high-quality economic development. This paper took 108 cities in the Yangtze River Economic Belt as the research objects and used the super-efficiency SBM model considering unexpected output and the Malmquist index method to calculate carbon emission efficiency. Natural segmentation method of ArcGIS10.7 and Theil index were used to analyze the spatio-temporal evolution characteristics and regional differences. Finally, spatial Durbin model was constructed to further explore the influencing factors of carbon emission efficiency. The results showed that: (1) From 2005 to 2020, the carbon emission efficiency showed a fluctuating trend, and the overall carbon emission efficiency of the Yangtze River Economic Belt was insufficient. The efficiency level was greatly affected by technology and scale. (2) Malmquist index showed that the key reason for the significant gap of carbon emission efficiency among regions lied in the complementarity and mutual promotion of various efficiency indexes and the imbalance of emission reduction technology development. (3) The number of cities with the highest and higher carbon emission efficiency zones increased, and the agglomeration status of the Yangtze River Economic Belt was gradually becoming apparent. (4) Except for the level of economic development, other factors demonstrated significant positive or negative direct effects on carbon emission efficiency. The spatial spillover effects of economic development level, industrial structure, green technology innovation, and government intervention on carbon emission efficiency were indicated as significant factors.