Abstract: Aiming at the achievement of carbon peak and carbon neutrality goals, cities are becoming the main battlefield for energy conservation and carbon reduction. Therefore, study of the impact of urban spatial element distribution and single center multi center structure on carbon emission efficiency is of very important practical significance. This article took 41 cities in the Yangtze River Delta as the object. Firstly, based on the carbon emission data obtained from energy consumption calculations, the super efficiency SBM model was used to calculate the carbon emission efficiency of various cities. Then, the internal spatial structure of cities was measured based on nighttime light data. Finally, the impact, heterogeneity, and mechanism of the internal spatial structure of cities on carbon emission efficiency were analyzed using urban panel data from 2006 to 2019. Overall, the diffusion and development of cities towards multiple centers had a significant promoting effect on reducing carbon emissions and improving carbon emission performance. The impact of multiple centers on carbon emissions demonstrated a phased characteristic. As the urban form evolved from single center to multiple centers, carbon emissions first increased and then decreased, and carbon emission efficiency first suppressed and then improved. Heterogeneity analysis found that the carbon emission reduction effect of multiple centers was scale-dependent. Small cities were more conducive to carbon emission reduction through single center polarization development, while medium-sized and large cities had better carbon emission performance when developing towards multiple centers. The development of transportation facilities had a negative masking effect on the carbon emission reduction effect of multiple center cities, and the well-developed road transportation facilities in multi center cities increased the total carbon emissions; The development of cities towards multiple centers can optimize industrial structure, achieve improved production efficiency, energy conservation and emission reduction, and improve carbon emission efficiency.