Capital flow and logistics are closely linked in the supply chain. Current research primarily assesses their independent resilience during disruptions, but this study reveals an iterative bidirectional impact. The interconnection of shareholding, mutual guarantees, and borrowing within the supply chain has created financial relationships that were previously nonexistent. However, the evolution of logistics has not aligned with these financial developments, leading to a growing heterogeneity between capital flow and logistics. While the heterogeneity between capital flow and logistics within supply chains is crucial, previous studies, especially those rooted in complex networks, often overlook its impact. Drawing inspiration from the cyber–physical system, this paper abstracts logistics and capital flow into respective networks. A model of mutual dependence quantifies reciprocal impacts between capital and logistics networks, exploring the consequences of heterogeneity on the supply chain. Simulation results are compared with traditional single-layer network models. Finally, an innovative edge removal method is proposed to enhance supply chain robustness. Our simulation results indicate that the influence of the capital network on the logistics network and their relationship to heterogeneity is nonlinear. The edge removal method enhances supply chain network robustness in a nonlinear manner, with optimal effectiveness achieved at p_l=0.2.