BACKGROUND The COVID‐19 outbreak caused short‐term disruptions in the supply chain of fresh agricultural products (FAPs), which exposed the vulnerability of the existing FAP supply chain. With pandemic control being widely coordinated, the supply chain of FAPs was gradually optimized and improved. However, after the outbreak of COVID‐19, achieving an effective supply of FAPs in future pandemics has become a key issue. The present work therefore aimed to construct a three‐level supply chain based on the Stackelberg game model, consisting of suppliers, third‐party logistics (TPL), and retailers, to guarantee the supply of FAPs. COVID‐19 pandemic factors such as virus infection coefficients and pandemic prevention efforts were fully integrated into the model. RESULTS Compared with the wholesale prices of FAPs, preservation efforts and pandemic prevention efforts have huge impacts on the retail prices of FAPs. When suppliers are in the leading position, the quality assurance effort level is positively correlated with the optimal profit. Compared with this situation, when FAP retailers are in the leading position, TPL providers show higher levels of pandemic prevention effort and FAP preservation effort. With an increase in consumer preference for pandemic prevention, the profits of supply‐chain members when FAP retailers are in the leading position will gradually increase. CONCLUSION This study reveals an effective supply mechanism for FAPs in metropolitan areas during the COVID‐19 pandemic and describes the authors' experience of guaranteeing the quality and safety of FAPs for future pandemic cases. © 2021 Society of Chemical Industry.