Based on panel data from Sichuan Province and its 21 prefecture-level cities spanning 2013 to 2022, the super-efficiency SBM model was utilized to assess agricultural eco-efficiency. This model incorporates non-expected outputs. Spatiotemporal differentiation was analyzed using ArcGIS software, and influencing factors were examined using the Tobit regression model. The results revealed that: (1) Agricultural eco-efficiency in Sichuan province demonstrated a pattern of fluctuating growth throughout the ten-year period, with the five economic zones exhibiting distinct hierarchical characteristics: Northwest Sichuan Ecological Demonstration Zone > South Sichuan Economic Zone > Panxi Economic Zone > Northeast Sichuan Economic Zone > Chengdu Plain Economic Zone. (2) Prefecture-level cities throughout Sichuan Province exhibit significant spatial heterogeneity and imbalance, characterized by a distribution pattern where the "central and western regions display higher levels, while the eastern region is lower". (3) Irrigation rates and farmers' income levels significantly positively impact agricultural efficiency, whereas mechanization, industrialization levels, and fiscal support for agriculture exhibit a negative influence. To enhance agricultural ecological efficiency and foster high-quality modern agricultural development in Sichuan Province, strategies are recommended to optimize the agricultural structure by coordinating regional low-carbon ecological initiatives. Additionally, refining the fiscal support framework for agriculture to emphasize ecological considerations is crucial.