In view of the phenomenon of different market segments and different levels of government subsidies for agricultural products, optimization suggestions and government subsidy strategies for the improvement of the supply and demand of sustainable agricultural products and environmentally friendly agricultural products are proposed. Based on the assumption that the government adopts differentiated subsidies for three heterogeneous manufacturers and the comprehensive consideration of the properties of agricultural products and the different preferences of consumers, Stackelberg game theory is used to establish a supply and demand model under the sustainable supply chain of agricultural products and the government formulates the optimal subsidy policy according to the goal of maximizing social welfare to further promote the equilibrium of supply and demand in the market segments of the sustainable supply chain. Finally, the influence of various parameter perturbations on the correlative optimal decision results is analyzed by numerical simulation. The results show that the government’s subsidy policy can effectively reduce the price of agricultural products, increase market demand for environmentally friendly agricultural products and sustainable agricultural products, and improve consumers ’ sustainable consumption levels, which is conducive to achieving a win-win situation for economic and environmental benefits. It has certain guiding significance and reference value for the sustainable and coordinated development of the supply chain.