Abstract: Agricultural ecological efficiency is an important index to measure agricultural sustainability, which is one of the important issues affecting agricultural sustainable development in China. Based on the data of 9 provinces and 2 cities in the Yangtze River Economic Belt from 2008 to 2019, the undesirable two-stage network Super- NSBM model was used to measure the agricultural ecological efficiency and its stage efficiency, and the spatial and temporal characteristics and influence mechanism of regional agricultural ecological efficiency were investigated by using the kernel density analysis method and Tobit model. The results show that: (1) During the study period, the average agricultural ecological efficiency is less than 1, below the effective value, 0.932,0.845 and 1.117 7 in the upper, middle and down-stream, respectively, showing a trend of down-stream > upper stream > middle stream, with significant differences among provinces and cities. (2) From the regional perspective, only Jiangsu Province achieved DEA efficiency in two stages.Jiangxi, Guizhou, Shanghai and Sichuan are weak DEA efficient provinces. (3) Agricultural ecological efficiency and its stage efficiency are positively affected by agricultural mechanization level, agricultural planting structure adjustment, and negatively affected by the agricultural disaster rate. The degree of agricultural marketization and the level of financial support for agriculture have a positive impact on the efficiency value of the agricultural ecological governance stage.