Abstract: Considering the impact of green goodwill on profit of green supply chain, a study is conducted on the collaborative innovation cooperation of green supply chain composed of a single core enterprise and a single supporting enterprise with the method of differential game. To be specific, in the cases of non-cooperative contract, cost-sharing contract and cooperative contract, the optimal green innovation inputs of the core enterprise and the supporting enterprise, their respective optimal profits and the overall optimal profit of green supply chain are respectively investigated. Through a comparative analysis, it is found that: 1) as an incentive mechanism, the cost-sharing contract can improve the green innovation input of the supporting enterprise, the optimal profit of both parties and the overall profit; 2) under the cooperative contract, the overall profit of green supply chain and the green innovation input of both parties are optimized. The research conclusions provide the theoretical basis for the effective collaborative innovation cooperation between the core enterprises and the supporting enterprise in green supply chain.