Abstract: In response to the strategic call for the "Great Protection" of the Yangtze River Economic Belt and to fulfill the important historical tasks assigned by the state to the provinces and cities of the area, the Yangtze River Economic Belt is adjusting the agricultural industry structure, optimizing the input-output ratio, and ensuring stable and sustainable agricultural production. Based on the combination of the three-stage Data Envelopment Analysis (DEA) model and cluster analysis, this study examined the Yangtze River Economic Belt from 2008 to 2018 to measure its agricultural production efficiency and to analyze its temporal and spatial characteristics. Studies shown that exogenous environmental factors significantly (P < 5%) impact agricultural production efficiency in the Yangtze River Economic Zone, and there were temporal and spatial differences. These include: 1) after excluding environmental factors, the overall agricultural production efficiency of the Yangtze River Economic Zone had improved. Sichuan and Jiangsu Provinces were at the forefront of efficiency, whereas the agricultural production efficiency of Shanghai had obviously declined. 2) The agricultural production efficiency of the Yangtze River Economic Belt varied year by year, with fluctuating development. The middle reaches of the Yangtze River had advanced agricultural production efficiency more than the upstream and downstream regions, and the agricultural production efficiency of the individual provinces did not match their economic and social development. 3) Increases in labor, land, irrigation, and other input factors increased agriculture production efficiency, there was no correlation between fiscal investment per capita gross domestic product (GDP) and agricultural production efficiency. The disaster-affected area had a significant negative impact on agricultural production efficiency.