We analyze the effects of the multi-layer network structures on the proliferation of industrial cluster risks and demonstrate the effects by multiple cases. With the help of computer simulation, we depict the dynamic evolution of cluster structures during the proliferation of exogenous and endogenous risks. We conclude that both Marshallian cluster and hub-and-spoke cluster have higher resistance to exogenous risk than to endogenous risk, and that Marshallian cluster has higher resistance to endogenous risk than hub-and-spoke cluster, while hub-and-spoke cluster has higher resistance to exogenous risk than Marshallian cluster.