The problem of difficult and expensive financing of credit funds restricts the development of agriculture in our country. The government adopts different measures to support and guide the sustainable development of agriculture, there are typical loan interest subsidy mechanism. Under the background of agricultural output is uncertain, a supply chain system composed of farmer, company, bank and the government has been established, it discusses the government subsidy for agricultural supply chain operation and the influence of the members of the decision-making, explores the differences between two kinds of mechanism and provides suggestions for the decision of the supply chain members. Studies have shown that in the context of government subsidy, when the random output factor is higher and the loan interest rate is lower, the higher the loan interest subsidy rate, the higher the profit and social welfare of farmer, company, and bank. When the bank interest rate is higher than a certain value, the government subsidy can increase the profits of farmer and bank. Finally, numerical simulation found that in the context of government subsidy, government subsidy reduces the financing cost of farmer, but the real beneficiary is bank.
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