Abstract: Taking 35 prefecture-level cities in the Huaihe River Basin from 2001 to 2020 as the research objects， non-point source pollution and carbon emission indicators were integrated， and the super-efficiency EBM model， Theil index， and panel Tobit regression model were adopted to reveal the spatiotemporal evolution and driving mechanisms of agricultural ecological efficiency （AEE）. The results showed that：（1） Temporally， AEE exhibited a fluctuating upward trend， but substantial space for optimization remained；（2） Spatially， the efficiency gap continued to converge， with the distribution transforming from dispersion to balanced optimization； high-efficiency areas were significantly agglomerated in the junction zone of Henan， Anhui， and Shandong provinces， forming an "edge rise"， while block-shaped efficiency depressions emerged in central Henan and northern Anhui； intra-provincial differences were the dominant source of regional differentiation， among which the internal differentiation within Anhui and Henan provinces was the most prominent； （3）Regarding the influencing factors， the urbanization， multiple cropping index， grain cultivation， irrigation conditions， and large-scale operation improved efficiency through resource integration， while fiscal support for agriculture （subsidizing high-carbon factors）， mechanization （reliance on fossil energy）， and the structure of scientific and technological expenditure （neglect of green technologies） exerted significant inhibitory effects due to deviations in policy orientation. In the future， it is necessary to deepen the quantitative analysis of inter-provincial institutional barriers and innovate governance paths.