With the proposed goals of reaching its “carbon peak” by 2030 and becoming “carbon neutral” by 2060, China will comprehensively build a diversified, efficient and clean energy system. The differences in China’s resource endowments have made the development of carbon emission reduction in the thermal power industry uncoordinated in various regions. Therefore, it is necessary to optimize the method for measuring thermal power carbon emission efficiency and determine the impact of regional development imbalances on the carbon emission efficiency of thermal power. For this article, we used the stochastic frontier analysis method and selected a variety of influencing factors as technical inefficiency items. After that, we measured the thermal power carbon emission efficiency in 30 provinces and municipalities (autonomous regions) in China in the past 10 years, and it was found that the efficiency was increasing yearly and showed obvious spatial differences. The impact of the clean energy substitution effect on the thermal power carbon emission efficiency cannot be ignored. After performing a coupled and coordinated analysis on the efficiency of thermal carbon emission in various regions and its influencing factors, the three indicators of power consumption intensity, urbanization level and clean energy substitution effect were selected. The weight of the indicator subsystem was determined in view of the estimation of the technical inefficiency. The results of the coupling and coordination analysis show that the degree of coupling and coordination of thermal power carbon emission efficiency is increasing yearly and presents a distribution of “high in the eastern region and low in the western region”. Therefore, all provinces need to vigorously carry out clean replacement work to enhance the coordinated development of carbon emission reduction in the thermal power industry and the level of regional economic development.