Cross-regional, cross-industry and cross-organization integration has become an important development trend. It is of great significance to analyze the risk propagation process and explore the strategies to improve the invulnerability of the cross-boundary integrated supply chain networks to cope with the risk shocks and achieve safe and stable development. Based on the reality of cross-boundary cooperation among some enterprises distributed in different industrial fields, this study constructs a risk propagation model of the cross-boundary integrated supply chain network from the perspective of multilayer networks, then simulates and analyzes network invulnerability based on network structure and recovery strategy. The results show that: 1) The cross-boundary integrated supply chain network under the partial dependency mode has stronger invulnerability; 2) When core supply chain enterprises or cross-boundary team enterprises are shocked by risks, the decline in network invulnerability is more obvious; 3) There is a marginal diminishing effect on the recovery benefit of network recovery strategies; 4) The invulnerability recovery effect of cross-boundary integrated supply chain network under the fully dependent mode is better than that of the partial dependent mode; 5) Adjusting the parameters of the risk propagation model can improve the network invulnerability and inhibit the large-scale spread of risks within a certain range.