In view of the difficulty of financing for small and medium-sized enterprises and the moral risk in supply chain finance, the principal-agent theory was adopted to make appropriate incentive contracts for the financing mode of government procurement contracts proposed by the Ministry of finance. Based on the principal-agent theory, a two-layer principal-agent model of government procurement departments, third-party logistics enterprises and small and medium-sized enterprises winning the bid was constructed. The model was then analyzed and solved. Based on the above solutions, Matlab software was used to conduct simulation experiments to verify the influence of different parameters on the change of incentive contract. It is found that the enterprise's effort level under the condition of information asymmetry is less than that under the condition of information symmetry. By increasing the effort output coefficient and decreasing the effort cost coefficient, the effort level and incentive remuneration can be improved. By reducing the risk aversion of enterprises and paying close attention to exogenous random factors outside the market, the generation of general agency costs can be reduced.