Rural governing structure changes with the strategic objective of the state's development. It is unrealistic to analyze the rural governing structure independently. It is suggested to respect the economic poverty and scattered residence features of traditional small farmers, explore the reasons of the priority on military and heavy industries in the initial developing stage of New China. This will facilitate the "Rural-Urban inequality" and to build the citizen society. Based on the analyze of the reasons, characteristics and rules of rural governing structure in modern China, this paper proposes some suggestions on promoting agricultural and rural development, so as to promote to build a harmonious society.