Objective From the perspective of the government on food safety regulatory functions to seek a connecting point between public health emergencies and food security，to build emergency management mechanisms dealing with public health emergencies in rural areas. Methods Through designing a government crisis management function to integrate and upgrade an emergency system under food security crisis. Results In the management of public health emergencies in rural areas，food security and food safety system of the government play an important role in improving the emergency response mechanism. Conclusion Establishment of a mechanism dealing with public health emergencies in rural areas needs to redefine the responsibility of the government to achieve an organic coordination of macro-functional management and micro-system design.