A public health crisis is a "touchstone" for testing the ability and capacity of rural and urban health systems. In the context of coronavirus disease 2019 (COVID-19) in China, we track the features, challenges, and implications of the temporary disruption of the health system in rural China and its response to this major public health crisis. We examine the general content and logic of village pandemic prevention and control regarding COVID-19 through a case study. Accordingly, we identify the challenges to the rural health system, including logic failure and its causes. It is strongly suggested that the government strengthen rural health system reform, balance medical services between rural and urban areas, and strengthen public health awareness and education.