Abstract: Seed industry innovation is a key driver for enhancing the resilience of the agricultural industry chain and plays a strategically important role in ensuring food security and promoting agricultural modernization. Based on provincial panel data from China spanning 2012–2021, this study constructs a measurement system for agricultural industry chain resilience and systematically examines the effects of seed industry innovation, its internal mechanisms, and heterogeneity. The results show that: 1) seed industry innovation significantly enhances the resilience of the agricultural industry chain, and this conclusion remains robust after addressing endogeneity concerns; 2) mechanism analysis reveals that seed industry innovation strengthens industry chain resilience through dual pathways of chain extension and chain reinforcement; 3) heterogeneity analysis indicates that the promoting effect of seed industry innovation is more evident in non-grain production functional areas and regions with high resilience levels of the agricultural industry chain; 4) results of the dual threshold model demonstrate that as regional economic development and rural human capital improve, the promoting effect of seed industry innovation on agricultural industry chain resilience exhibits a nonlinear enhancement trend. Based on these findings, it is suggested to establish an innovation-targeting anchoring mechanism to enhance the transmission efficiency of chain extension and reinforcement, implement spatially adaptive gradient empowerment strategies for seed industry innovation, and improve the dynamic adaptation mechanism between human capital and regional development.