Currently, the integrated development of agriculture and tourism is one of the most critical strategic measures in China. The rapid growth of agricultural tourism integration presents the typical characteristics of expanding regional differences. Exploring the impact of agricultural tourism integration on the growth of green total factor productivity in agriculture has important theoretical and practical significance. This study constructs a comprehensive index system for agricultural tourism integration, measuring the development level of agricultural tourism integration in 30 sample provinces from 2008 to 2018. Using the generalized system method of moments approach and Tobit model, the impact of agricultural tourism integration on agriculture was empirically tested, and the regulatory role of rural human capital was discussed. It was found that agricultural tourism integration contributes significantly to the improvement in green total factor productivity in agriculture, with rural mobility human capital, education human capital, and health human capital all playing a significant positive moderating role in this process. Finally, it is recommended that priority be given to agricultural tourism integration in the policy framework, promoting industrial chain upgrading, raising investment in rural infrastructure, and upgrading rural human capital levels to contribute the rural economic development.