In recent years, international public health emergencies have occurred frequently, which severely affect shipping and trade exchanges between the affected areas. In particular, the stagnation and conversion of refrigerated containers affected by the pandemic prevents the demand for cold chain goods from being continuously met. At the same time, viruses adhere to the cold chain environment. As a result, the risk of transmission is relatively high. Therefore, it is necessary to study the optimization of international cargo transportation routes in a pandemic. Based on the designated cold storage mode of the first station, scientific planning for the transportation of refrigerated containers is conducted, and the safe and efficient transportation of cold chain goods is finally realized, aiming to minimize the transportation cost of refrigerated containers and the shortest transportation completion time, and establish a dual-objective optimization model for reefer container transportation route planning under the epidemic situation. The transportation volume of refrigerated containers on routes and ship schedules is determined by the real-time transportation volume sent from the destination port to the secondary cold storage during the land transportation phase. Asian ports A and B that have cold-chain goods with China are selected as the import locations, and domestic ports C and D that have a large overlap in hinterland demand are selected as the transportation route nodes for refrigerated containers. According to the established transportation routes, schedules, ship information and freight rates and other data are used to optimize the route planning of the refrigerated container transportation route in the marine and land transportation stages, and the non-dominated sorting genetic algorithm with elite strategy (NSGA-II) is used to solve the problem. The calculation results show that when the detection capability is 20TEU, the transportation cost of the refrigerated container is USD $44 210 to 75 350, and the transportation time is 1 422 to 3 000 h. The route analysis is conducted on one group of Pareto optimal solutions, and it is found that the route selection in each cycle is different. The first stop sensitivity analysis is performed on the detection capability of the designated cold storage. When the detection capability Aj is 20, the maximum transportation completion time is 3 000 h. When the detection capability Aj is expanded to 50, the maximum transportation completion time is 2 280 h, and the transportation completion time is reduced by 24%. The results show that the greater the detection capability of the first station designated cold storage, the smaller the total transportation time, but when the detection capability reaches a certain value, the impact on the entire cold chain transportation process is no longer significant.