Abstract: The synergy between the Water-Energy-Food system and agricultural total factor productivity in the Yangtze River Basin is crucial for high-quality agricultural development. Taking 10 provinces and municipalities in the Yangtze River Basin as the research subjects, this study combines the panel entropy-weighted TOPSIS model, super-efficiency SBM model, and coupling coordination degree model to reveal the spatiotemporal evolution patterns of the coupling coordination between rural household water-energy-food and agricultural total factor productivity from 2006 to 2022. The LASSO-XGBoost-SHAP model is used to identify key driving factors. The research results indicate that the coupling coordination degree in the basin shows a continuous upward trend, with a significant acceleration in growth after 2018. In terms of spatial characteristics, the coordination degree in the downstream region has long been leading, the midstream region has leaped from moderate imbalance to primary coordination, and the upstream region has shifted from polarization to synergistic improvement. Regarding the driving mechanisms, per capita GDP is the core driving force across the entire basin, but there is significant regional heterogeneity: the downstream region relies on the synergy between economy and technology, the midstream region is constrained by water resource management, and the upstream region faces ecological constraints. Based on these findings, recommendations are proposed to promote efficient water-saving technologies and optimize cross-regional water resource allocation, bridge the upstream-downstream gap and reduce regional disparities, and establish a basin-wide coordination mechanism with innovative differentiated technical tools.