Based on the context of enterprise green innovation ecosystem, this paper discusses the decision-making of knowledge innovation and environmental social responsibility in the multi-agent enterprise R&D innovation system that is composed of core enterprises and satellite enterprises, and it provides a new perspective for comprehensively improving enterprise innovation ability. By using differential game method and considering the joint influence of knowledge innovation and environmental social responsibility, this paper analyzes the cooperative innovation of multi-agent enterprises under a dynamic framework and discusses the decision-making process and optimal returns of core enterprises and satellite enterprises under centralized decision, decentralized decision and Stackelberg master-slave game modes. The conclusions are as follows: (1) When multi-entity enterprise R&D and innovation system moderately fulfill their environmental social responsibilities, their income increases significantly, and the green innovation capability of green innovation ecosystem is enhanced effectively; (2) When the profit ratio of core enterprises is controlled above 1/3, and the subsidy rate of government on satellite enterprises is controlled below 2/3, the green innovation ecosystem is in a balanced state, and the innovation initiative of multi-agent enterprises reaches a high level; (3) Under centralized decision making, the revenue proportion of core enterprises decreases, but the overall revenue of R&D innovation system reaches the Pareto optimum. Finally, the differential game decision-making process is analyzed with an example to verify the validity of the model conclusion, which provides a scientific basis for the knowledge innovation decision of multi-agent enterprise R&D innovation system in the green innovation ecosystem and accelerates the process of carbon neutrality.INDEX TERMS Carbon neutral, green innovation ecosystem, knowledge innovation, environmental social responsibility, differential game.