In China’s emergency plan system，the primary epidemic prevention emergency plan is in the function of early emergency disposal，which is very important for epidemic prevention and control. However，in the actual operation，there are some institutional obstacles in the grassroots epidemic prevention emergency plan，such as the weak early-warning mechanism，the alienation of early warning mechanism，the lack of legal protection and so on. In order to meet the needs of public epidemic prevention and control，improve the response efficiency of epidemic prevention and control，and assist the superior epidemic prevention and control work，China should gradually change from the top-down central leading mode to the top-down linkage multi governance mode. Therefore，this paper puts forward some specific ways to improve the operation efficiency of the grassroots emergency plan，such as strengthening the early disposal function of the grassroots emergency plan，reshaping the early warning mechanism of the grassroots epidemic prevention and control，and supplying the legal resources of the grassroots emergency plan.