Factor endowment structure has a direct influence on the agricultural moderate scale management. By constructing the Endowment Structure Model of agricultural land, labor and capital variables, the dynamic mechanism of agricultural moderate scale management and the impact of excessive government intervention in factor market on agricultural moderate scale management can be revealed in the evolution process of factor endowment structure. Agricultural moderate scale management aims to realize rational allocation of land, labor and capital and so on under the factor endowment structure and to change with the rising of factor endowment structure. Excessive government intervention with factor market certainly leads to agricultural business scale to deviate from agricultural factor endowment structure, and the policy of government to boost agricultural moderate scale management must be established on the premise fitting for factor endowment structure. In order to propel China’s agricultural moderate scale management, currently, government should provide necessary infrastructure, make great effort to create open, free and competitive market environment, cultivate self-existence viability of agricultural production units and set up and perfect the matched insurance system and compensation system to reduce the risk of agricultural scale management.