In order to ensure the continuous supply and effective allocation of emergency materials, enable the supply chain of emergency materials to maintain a certain supply capacity when the supplier fails, respond quickly and recover to a good operating state, and thus improve the efficiency of emergency management, this paper introduces the theory of resilience into emergency materials supply chain decision-making for natural disasters. Based on the resilience prevention strategies (capacity reserve and multi-source procurement), resilience response strategy (standby suppliers) and resilience recovery strategy (original supplier capacity repair), a two-stage mixed-integer stochastic programming model encompassing pre-disaster and post-disaster phases with the goal of minimum total supply chain cost and maximum total supply chain resilience is established under the premise of the government-enterprise joint model. The decision-making solutions for the emergency supply chain under different scenarios and multiple uncertainties are derived through numerical example analysis. The validity of the model and the applicability of the resilience strategy are proved by comparative analysis and sensitivity analysis. The results show that the resilience strategy can effectively improve prevention, response and recovery abilities of the supply chain to cope with supply interruptions. The resilience prevention strategy is only applicable when the degree of supplier failure is small. The longer the supplier’s failure time and the greater the degree of failure, the greater the role played by the standby supplier, conversely, the greater the role played by the original supplier’s capacity repair.