As the backbone of China's regional development pattern, increasing carbon efficiency in the middle reaches of the Yangtze River urban agglomeration is of great significance to help China achieve the "double carbon" goal. In order to explore the carbon efficiency differences and influence paths of each region in the middle reaches of the Yangtze River urban agglomeration and propose corresponding improvement strategies, we applied a three-stage SBM-DEA model to measure the carbon efficiency of 28 cities in the middle reaches of the Yangtze River urban agglomeration from 2006 to 2019 and analyze the impact of environmental variables, which excluded the influence of external environment and random factors. Then, we also used kernel density estimation and center-standard deviation ellipses to analyze the spatial and temporal evolution of carbon efficiency, which aimed to find a site-specific approach to make targeted suggestions for carbon efficiency improvement. The results show that: ① the overall carbon efficiency of the middle reaches of the Yangtze River urban agglomeration is not high but shows a trend of the fluctuating upward year by year. There is no GDP output redundancy among cities, and the main reasons affecting carbon efficiency in the middle reaches of the Yangtze River urban agglomeration are focused on capital, labor, energy inputs, and CO2 emissions. ② The carbon efficiency of the middle reaches of the Yangtze River urban agglomeration shows a spatial divergence pattern of Wuhan city circle > Changzhutan urban agglomeration > Poyang Lake urban agglomeration, while the center of efficiency moves to the northeast. The standard deviation of the long axis of the standard deviation ellipse decreases as a whole, and the standard deviation of the short axis is relatively stable. The overall area of the standard deviation ellipse has decreased, which means that the difference in carbon efficiency between regions is reducing year by year. ③ There is a positive spatial spillover effect of carbon efficiency in the middle reaches of the Yangtze River urban agglomeration, and the urbanization process, industrial structure, and technology support intensity are crucial factors affecting carbon efficiency. Within the middle reaches of the Yangtze River urban agglomeration, Wuhan city circle, Changzhutan urban agglomeration, and Poyang Lake urban agglomeration have some competitive relationship in capital, labor, and energy input. Therefore, the better-developed areas siphon resources to the surrounding areas, which formed the negative spatial spillover effect within the middle reaches of the Yangtze River urban agglomeration.