Realizing the green development of agriculture is an important foundation for the sustainable development of the economy and society. In China, rural industrial integration is a major innovation in the development of rural productivity in the new development stage, which is of great significance for promoting the green development of agriculture and enhancing the green total factor productivity of agriculture. Based on the panel data of 30 provinces in China from 2010 to 2021, the super- SBM method was used to estimate agricultural green total factor productivity (AGTFP), and the comprehensive index method and entropy method were used to measure the level of rural industrial integration. Based on the spatial autoregressive model with a spatial autoregressive error term (SARAR model), intermediary effect model and threshold effect model with a spatial autoregressive error term, the influence and mechanism of rural industry integration on AGTFP were demonstrated. The results show that (1) there is a significant positive relationship between the development level of rural industry integration and AGTFP; that is, the development of rural industry integration can effectively promote the improvement of AGTFP and promote the green development of agriculture. Considering the spatial effect and endogeneity, the robustness test based on the generalized spatial two-stage least square method (GS2SLS) further strengthens the above mentioned conclusion. (2) Rural industrial integration has a significant scale effect, capital effect and technology effect; that is, rural industrial integration mainly promotes AGTFP indirectly by promoting agricultural scale management, improving rural human capital and promoting agricultural technological progress. (3) The influence of rural industry convergence on AGTFP has the characteristics of a single threshold. With the improvement of the integration level, the influence of rural industry convergence on AGTFP shows an increasing trend. Therefore, China should strengthen the deeply integrated development of rural industries, promote the appropriate scale operation of agriculture and the adjustment of planting structure, accelerate the process of agricultural technology innovation and rural human capital accumulation, and realize the win-win situation of rural economic and ecological construction.