Reducing and sequestering agricultural carbon is a crucial measure for achieving carbon neutrality and carbon peak, as well as an integral component of agricultural modernization. This study uses the super-efficiency Slack-based measure-Data envelopement analysis (SBM-DEA) and Exploratory spatial data analysis (ESDA) models to examine the spatiotemporal differentiation characteristics of agricultural ecological efficiency (AEE) in 38 districts and counties of Chongqing. The results indicate that the CRR-DEA model disregards the impact of undesirable output factors and overestimates the actual utilization of agricultural resources, whereas the super-efficiency SBM-DEA model is more consistent with the actual agricultural production process. Chongqing’s AEE was at a high level of efficiency and the distribution of spatial pattern is uneven, displaying a development pattern of “The urban agglomeration in the Three Gorges Reservoir area of Northeast Chongqing (UTC)>Main urban metropolitan area (MUA) > Wuling Mountain urban agglomeration in southeast Chongqing (WUC)”, and there is a significant agglomeration characteristic among various districts and counties. The High-High (H-H) agglomeration is primarily concentrated in the central urban area and the Low-Low (L-L) agglomeration area is primarily located in the eastern portion of UTC. Consequently, all regions in Chongqing should combine their own agricultural development characteristics, maximize their strengths, compensate for their weaknesses, and thereby enhance the AEE.