Rural governance is the necessary basis of national governance,which is related to the success of the modernization of national governance.Under the trend of rural atomization in China,rural governance in ethnic areas is in a dilemma.By analyzing the main bodies of atomized rural area governance in ethnic minority areas and their roles in rural area governance,this paper probes into the difficulties and causes in atomized rural area governance in ethnic minority areas,and finally discusses the strategies of realizing the modernization of this kind of governance,so as to promote the early realization of national governance modernization and rural revitalization.