Achieving urban-rural integration and deep integration of urban and rural areas is an inherent requirement for the high-quality development of China’s economy. The paper analyses the spatial and temporal evolutionary characteristics of the coupling and coordination of the urbanization system and the rural ecological environment system (referred to as the two systems) in the Yangtze River Economic Belt, and empirically tests the influencing factors of their coupling and coordination using a panel Tobit random effects model. The results show that: (1) the coupling degree of the two systems presents antagonistic characteristics from 2001 to 2019. The coupling coordination degree has advanced from moderate dissonance at the beginning of the period to slight coordination, showing a good trend of steady improvement. (2) Financial support to agriculture, rural economic development, science and technology innovation, and government governance capacity have a significant positive effect on the coupled and coordinated relationship between the two systems, while environmental regulation has a significant negative effect on them. Except for government governance capacity, all the other four factors show significant regional heterogeneity. (3) Finally, policy insights are given in terms of optimizing financial support policies for agriculture, enhancing the government’s capacity for collaborative governance, gathering elements of scientific and technological collaborative innovation, and positioning for differentiated development, with a view to providing references for decision-making in promoting the integrated ecological development of the Yangtze River Economic Belt and the integrated and coordinated development of urban and rural areas.