Abstract: Carbon emissions in China is of significant attention. Improvement of carbon emission efficiency in cities is crucial to balancing economic growth and environmental protection. This study employed the super-efficiency SBM model to assess the energy carbon emission efficiency of the Chengdu-Chongqing urban agglomeration from 2005 to 2022. The spatial and temporal evolution characteristics were also analyzed. A number of 16 cities in the study area were categorized based on the constructed influencing indicator system of energy carbon emission efficiency. A spatial panel model was used to investigate the drivers of energy carbon emission efficiency in different types of cities. The results showed that, from 2005 to 2022, the total carbon emissions of the study area increased at an average annual growth rate of 3.92%. The annual energy carbon emission efficiency showed a trend of decreasing and then fluctuating upward. The efficiency of Mianyang, Yibin, and Nanchong was not coordinated with the level of economic development. The efficiency of the Chengdu-Chongqing urban agglomeration exhibited a differentiated distribution pattern with high core and low periphery, and there was a multipolar phenomenon manifested by the fact that Chengdu and Chongqing were the high-value regions and the surrounding cities were the low-value regions. Economic development, industrial structure, energy intensity, and population distribution were identified as the factors affecting the improvement of carbon emission efficiency. However, the impact of investment scale, spatial layout, and urban planning on energy carbon emission efficiency differed according to the city type and the development stage. This study provided technical support for urban carbon emission reduction and policy recommendations for low-carbon development in the Chengdu-Chongqing urban agglomeration and other urban agglomerations.