Abstract: By constructing an AEE three-dimensional coupling development system of modern agriculture, regional economy, and ecological environment, this study analyzed the coupling and coordination degrees of the Yangtze River economic belt from 2000 to 2017 and evaluated the global and local spatial autocorrelation levels of the coordination degrees by calculating the Moran’s Index and Getis-Ord G Index. In addition, this paper also predicted the coupling degree of the AEE system of the Yangtze River economic belt from 2018 to 2022 based on the GM (1,1) model. Results show that: 1) the coupling degrees of the AEE system in 11 provinces of the Yangtze River economic belt are rising, but the development differences among regional subsystems are obvious; 2) the AEE system of the Yangtze River economic belt is dominated by the harmonic coordination class and the primary coordination class, which is in the transition from moderate coordination to high coordination with the distribution pattern of high downstream and low upstream and a narrowing gap between them; 3) under different matrix modes, there is a clear spatial correlation between the coordinated development level of the AEE system in the Yangtze River economic belt, which forms a hot spot in Zhejiang and a cold spot in Yunnan, and 4) it is expected that the coordination of the AEE system in the Yangtze River economic belt in the next five years (2018—2022) will maintain a benign development trend, but the development of the AEE system in the provinces of the river basin is still unbalanced. Therefore, to provide theoretical references for the integrated development of agricultural modernization, regional economic development, and ecological environment protection in the Yangtze River economic belt in the future, this paper suggests to carefully consider the characteristics of each subsystem and the coupling and coordination relationship among them.