Abstract:In this paper, three contractual models are constructed based on the innovative decision-making intention of the various subjects of the supply chain and the overall innovation interests of the supply chain under the background of cooperative research and development of industry, science and research. The research shows that under the situation of government subsidy, the interval selection of subsidy ratio determines the incentive effect, the two-way punishment contract has no effect on the decision-making of the cooperative supply chain of industry, education and research, and the income sharing contract can effectively balance the distribution of profits upstream and downstream of the supply chain while improving the overall profit of the supply chain. The improvement of innovation ability is an important guarantee to promote the efficiency of innovation in cooperation between industry, science and research, and the rational use of effective incentive contract can further enhance the value promotion of innovation ability in the supply chain of industry, science and research.