The first priority of the structural reform of agricultural supply is to ensure effective grain supply. The core content is to adjust the structure of production and the key to success is to improve the quality of agricultural products. This reform can also promote the integration of primary, secondary and tertiary industries in rural area, adapt to the new situation of the development of agricultural production and the new change of the main contradiction of agricultural production, reduce inventory and energy consumption, and increase farmers’ income. However, currently, this structural reform faces many difficulties and challenges, including small scale operations, weak agricultural infrastructure, short agricultural industrial chain, lagged agricultural science and technology support and the insufficient subsidy policies. To accelerate the pace of the structural reform of agricultural supply side in China so that we can improve agricultural comprehensive benefit and competitiveness, increase farmers’ income, and protect agricultural ecological environment, this paper suggests that to increase the operation scales, to strengthen the construction of agricultural infrastructure, to promote deep integration of primary, secondary and tertiary industries in rural areas, to encourage innovations in the modern agricultural science and technology, and to perfect agricultural subsidy policies.