The spread of COVID-19 has affected not only public health but also agriculture, raising global concerns regarding the food system. As an immediate impact of COVID-19, farmers around the globe have had difficulties with sales, resulting in large amounts of overstocked agricultural products and food loss. This further threatens the livelihood of rural, poor farmers and impacts sustainable production. To provide a better understanding of the overstocking situation after the outbreak of the pandemic, this study depicts the distribution characteristics of overstocked agricultural products in China. After analyzing a nationwide data set collected from 3482 individuals/organizations by the Chinese Agri-products Marketing Association after the outbreak of the pandemic, we found that some of the initial prevention and control measures disrupted sales channels, and in turn, caused the farmers to suffer losses. The impact was more severe in perishable products and their production areas, as well as in poverty-stricken regions. Then, we identified China’s quick and effective actions to match the supply and demand. These findings suggest that emergency responses should coordinate the relationship between emergency actions and the necessary logistics of agricultural production. To prepare for the possibility of such shock in the future, the government should take actions to clear logistics obstacles for necessary transportation, keep enhancing the fundamental infrastructure and effective mechanism of the food supply chain, and actively include innovative techniques to build a more resilient food system.