The integration of agriculture and tourism has emerged as a potential strategy to boost agricultural productivity and promote sustainable rural development in China. This study investigates the impact of agricultural tourism integration (ATI) on agricultural green total factor productivity (AGTFP) in China, filling a research gap in understanding the complex dynamic nexus. We examine the mediating role of the agricultural industrial structure adjustment index (AISAI) and the threshold effects of ATI and human capital level (HCL) using a panel dataset of 30 Chinese provinces from 2011 to 2021. The empirical results reveal three key findings: (1) ATI has a significant positive impact on AGTFP growth; (2) the AISAI partially mediates the relationship between ATI and AGTFP; and (3) ATI and HCL have a double-threshold effect and a single-threshold effect on the ATI-AGTFP nexus, respectively. These findings suggest that the effectiveness of ATI in promoting AGTFP varies across different stages of integration and levels of human capital development. The empirical results contribute to the literature on rural development strategies by providing an in-depth understanding of how ATI influences agricultural productivity and sustainability. Based on these findings, we propose targeted policy recommendations to optimize ATI strategies and invest in human capital to improve the resilience and sustainability of rural economies in China.