To explore the optimal mechanism of emergency supply chain collaboration when an epidemic crisis occurs, we construct a tripartite evolutionary game model of emergency collaboration among the government, the retailer, and the supplier to explore the interaction of primary strategies and the impact of critical parameters on the evolution and stability of the system. We conduct simulation analysis based on the actual situation of China’s emergency supply chain development. The research results show that in the recognition period of the crisis, the government participates in emergency supervision and the retailer participates in emergency collaboration, but the supplier does not participate in emergency collaboration. However, in the containment period of the crisis, the government increases penalties, provides appropriate emergency subsidies, and improves the efficiency of emergency supervision, which are conducive to promoting the supplier’s participation in emergency collaboration. In the recovery period of the crisis, as the benefits of both the retailer and the supplier participation in emergency collaboration increase, the government will withdraw from emergency supervision gradually. Moreover, the weaker the risk of supply chain enterprises participating in emergency collaboration, the more reasonable the distribution of the collaboration benefits, and the more conducive to the spontaneous emergency collaboration of the retailer and the supplier.