China’s urban–rural dichotomy has resulted in a widening gap between urban and rural areas, posing significant challenges to rural development. This study aims to investigate the spatio-temporal differentiation and driving mechanisms of rural industry integration within the Chengdu–Chongqing Economic Circle in China. Using panel data from 2011 to 2020, we employed the entropy weight TOPSIS method to construct a comprehensive index that charts the evolution of rural industry integration across various districts and counties. Additionally, we utilized fixed-effect and spatio-temporally weighted regression models to analyze the underlying driving forces behind this integration. Our findings reveal a dynamic and varied landscape of rural industry integration, with different levels of depth and breadth across various subsystems. Spatially, we observed a transition from a dispersed to a more concentrated agglomeration pattern within the Chengdu–Chongqing Economic Circle. This shift suggests a diffusion effect emanating from core metropolitan areas, as well as an attracting force exerted by adjacent metropolitan circles. In terms of drivers, market demand, openness level, financial development, policy support, and agricultural insurance breadth significantly contribute to rural industry integration. However, technological progress and rural human capital exhibit a weaker correlation. Notably, our models identified pronounced spatial–temporal heterogeneity among these influencing factors, highlighting a nuanced and dynamic relationship between them. Overall, our study emphasizes the crucial role of rural industry integration in bridging the urban–rural divide and fostering sustainable agricultural development and rural revitalization. The insights gained from this research provide valuable guidance for policymakers and stakeholders seeking to optimize rural development strategies and unlock the potential of integrated rural industries.