The COVID-19 outbreak has exposed deficiencies in the supply chain of FAPs, which have also increased their vulnerability. As the COVID-19 epidemic continues to develop, the effective supply of FAPs during the epidemic prevention and control period has become a key part of the response to the epidemic in metropolitan areas. Based on the game theory, this study constructed a three-level supply chain consisting of suppliers, TPL service providers and retailers to guarantee the supply of FAPs in metropolises in the context of COVID-19 epidemic. By Stackelberg principle game theory, the optimal epidemic prevention effort level, preservation effort level, wholesale price, retail price and optimal profit result in the supply chain dominated by supplier and retailer are respectively solved. In this study, in addition to the characteristics of FAPs such as easy loss and perishable, COVID-19 epidemic factors such as virus infection coefficient and epidemic prevention efforts were fully integrated into the model to ensure the effective supply of FAPs in metropolitan areas. The main research conclusions are as follows. (i) In the context of COVID-19, compared with the wholesale prices of FAPs, the level of preservation efforts and epidemic prevention efforts will have a greater impact on the retail prices of FAPs in metropolitan areas. (ii) When the supplier is in the dominant position, the sensitivity coefficient of the quality assurance effort level is positively correlated with the optimal profit of the supplier. Compared with other members, they have stronger control ability and decision-making ability, so that their profits are greater than those of other members. (ii) Compared with suppliers who are in the leading position of guarantee and supply, when FAPs retailers are in the leading position of guarantee and supply, TPL service providers have a higher level of epidemic prevention efforts and preservation efforts for FAPs. At the same time, the quality effort level, market demand and retail price are all greater under the retailer-led guarantee. (iv) The profit of FAPs retailers is affected by the sensitivity coefficient of preservation effort level, epidemic prevention effort level and dominant guarantee status.The COVID-19 outbreak has exposed deficiencies in the supply chain of FAPs, which have also increased their vulnerability. As the COVID-19 epidemic continues to develop, the effective supply of FAPs during the epidemic prevention and control period has become a key part of the response to the epidemic in metropolitan areas. Based on the game theory, this study constructed a three-level supply chain consisting of suppliers, TPL service providers and retailers to guarantee the supply of FAPs in metropolises in the context of COVID-19 epidemic. By Stackelberg principle game theory, the optimal epidemic prevention effort level, preservation effort level, wholesale price, retail price and optimal profit result in the supply chain dominated by supplier and retailer are respectively solved. In this study, in addition to the characteristics of FAPs such as easy loss and perishable, COVID-19 epidemic factors such as virus infection coefficient and epidemic prevention efforts were fully integrated into the model to ensure the effective supply of FAPs in metropolitan areas. The main research conclusions are as follows. (i) In the context of COVID-19, compared with the wholesale prices of FAPs, the level of preservation efforts and epidemic prevention efforts will have a greater impact on the retail prices of FAPs in metropolitan areas. (ii) When the supplier is in the dominant position, the sensitivity coefficient of the quality assurance effort level is positively correlated with the optimal profit of the supplier. Compared with other members, they have stronger control ability and decision-making ability, so that their profits are greater than those of other members. (ii) Compared with suppliers who are in the leading position of guarantee and supply, when FAPs retailers are in the leading position of guarantee and supply, TPL service providers have a higher level of epidemic prevention efforts and preservation efforts for FAPs. At the same time, the quality effort level, market demand and retail price are all greater under the retailer-led guarantee. (iv) The profit of FAPs retailers is affected by the sensitivity coefficient of preservation effort level, epidemic prevention effort level and dominant guarantee status.