Abstract: Taking effective policy measures to promote the improvement of agricultural eco-efficiency is a major practical issue that is currently widely concerned by the government and academia. Based on the panel data of 238 prefecture-level administrative regions in China from 2002 to 2022, this paper uses the super-efficiency SBM model to measure agricultural eco-efficiency and reveal its spatial and temporal evolution characteristics. Using the multi-time point DID model, the pilot area of agricultural green development was taken as a quasi-natural experiment to explore its impact, heterogeneity and regulation mechanism on agricultural eco-efficiency. The results showed that: 1) China’s agricultural eco-efficiency increased from 0.039 in 2002 to 0.175 in 2022, showing a dynamic trend of increasing year by year. The clustering area of high agricultural eco-efficiency was dominated by South China, and it had evolved into a spatial pattern of multi-point flowering in Sichuan and Chongqing, Central China, Western China, Northeast China and South China. 2) Benchmark regression results showed that compared with non-pilot areas and before pilot implementation, pilot areas in pilot areas had a significant positive impact on the improvement of agricultural eco-efficiency, and the results had good robustness. 3) Regional differentiation analysis found that the impact of pilot areas on agricultural eco-efficiency was more significant in the eastern, coastal and major grain-producing areas. 4) The results of the adjustment mechanism test showed that the agricultural industry agglomeration and the diversification of crop planting structure played a positive role in promoting the improvement of agricultural eco-efficiency in the pilot area. Finally, this paper puts forward countermeasures and suggestions for orderly promotion of pilot areas and improvement of agricultural eco-efficiency.