Human food safety should be given priority during a major public health crisis. As the primary element of agricultural production, labor tends to suffer the most during a period of public health concern. Studying the impact of epidemic-affected labor shortages on agricultural production, trade, and prices has important implications for food security. This study used a calculable general equilibrium model to study the changes in agricultural production, trade, and prices under different labor damage scenarios. The results showed that agricultural production was less affected under a scenario where the epidemic was controlled locally. The output of agricultural products decreased by about 2.19%, and the prices of agricultural products increased slightly. However, the nationwide output of agricultural products decreased by only 0.1%, and the prices remained largely stable. In the case of the spread of the epidemic, the output of agricultural products in the epidemic area decreased by 2.11%, and the prices of certain agricultural products increased significantly. For example, the price of vegetables increased by 0.78%, the price of pork increased by about 0.7%, and those of agricultural products in other parts of the country also increased slightly. Compared with the national spread scenario, the local outbreak scenario had a smaller impact on Chinese food security, indicating Chinese effective policy against the epidemic. Although the impact of labor shortage under the influence of the epidemic on China was relatively limited, and considering its stable food security, we should pay attention to the increase in the process of agricultural products and changes in agricultural trade in the epidemic area. The residents in the epidemic areas could not effectively obtain nutritious food, which affected their health. Thus, the government should also completely mobilize agricultural resources to ensure the nutrition safety of residents during major public health incidents.