Against the backdrop of increasing global uncertainties, embedding into the FTA network has become an important strategy for a country to enhance the resilience of its industrial chain and improve its risk resistance capacity. This paper constructs a depth FTA network based on the heterogeneity of agreements and systematically analyzes its impact on industrial chain resilience, heterogeneous manifestations, and underlying mechanisms. The results show that a country’s enhanced position in the FTA network can effectively strengthen the resilience of its industrial chain. After a series of robustness tests, this result remains significant. The heterogeneity analysis indicates that, owing to their central positions in the FTA network, developed countries experience a more pronounced enhancement in supply chain resilience. At the same time, improvements in a country’s FTA network position exert particularly strong positive effects on the resilience of manufacturing and technology-intensive industries. Further analysis shows that an enhanced FTA network position can strengthen supply chain resilience by promoting linkages between domestic and foreign firms. Therefore, China should accelerate the construction of a high-standard free trade zone network, promote the coordinated development of domestic-invested and foreign-invested enterprises, and thereby enhance the resilience and security of the supply chain and industrial chain.