The impact of COVID-19 is global, and uncertain information will affect product quality and worker efficiency in the complex supply chain network, thus bringing risks. Aiming at individual heterogeneity, a partial mapping double-layer hypernetwork model is constructed to study the supply chain risk diffusion under uncertain information. Here, we explore the risk diffusion dynamics, drawing on epidemiology, and establish an SPIR (Susceptible–Potential–Infected–Recovered) model to simulate the risk diffusion process. The node represents the enterprise, and hyperedge represents the cooperation among enterprises. The microscopic Markov chain approach (MMCA) is used to prove the theory. Network dynamic evolution includes two removal strategies: (i) removing aging nodes; (ii) removing key nodes. Using Matlab to simulate the model, we found that it is more conducive to market stability to eliminate outdated enterprises than to control key enterprises during risk diffusion. The risk diffusion scale is related to interlayer mapping. Increasing the upper layer mapping rate to strengthen the efforts of official media to issue authoritative information will reduce the infected enterprise number. Reducing the lower layer mapping rate will reduce the misled enterprise number, thereby weakening the efficiency of risk infection. The model is helpful for understanding the risk diffusion characteristics and the importance of online information, and it has guiding significance for supply chain management.