The disequilibrium between supply and demand of agricultural products is a common problem being faced by many countries with severe novel coronavirus pneumonia. It has caused serious losses to agricultural producer income and urban consumer welfare. It points out the imbalance between the supply and demand of agricultural products in our country under the new crown pneumonia epidemic: the production end of agricultural products is difficult to sell, farmers suffer heavy losses, the consumption end of the agricultural product supply is tight, and the basic characteristics of residents welfare are damaged. This study uses uncertainty economics theory to comprehensively analyze the internal mechanism of the disequilibrium between the supply and demand of agricultural products in China. The results indicate that the outbreak of COVID-19 epidemic has brought serious uncertainty to the health and safety of practitioners engaged in the circulation of agricultural products, which was regarded as the main reason for the disequilibrium between supply and demand. The uncertainty was demonstrated by the dramatically increasing circulation cost of agricultural products and the enforced interruption of the transactions and logistics for some agricultural products. Therefore, it is suggested that government should implement insurance system for public health emergency, innovate the business model for agricultural products circulation, increase the temporary subsidy, release the epidemic risk level directly and train the antiepidemic ability for agricultural product circulation practitioners. These public efforts would reduce the additional cost caused by the uncertain factors such as epidemic situation, ensure the effective operation of supply chain for agricultural products, and guarantee the safety and stability of agricultural industry chain, which would be helpful to avoid the recurrence of the similar issue on disequilibrium between supply and demand.