This study introduces the concept of cooperative innovation into the supply chain management of green buildings. By leveraging theories such as externality theory, stakeholder theory, principal-agent theory, game theory, and incentive theory, and using a combination of theoretical and empirical methods, it closely aligns with the characteristics of the green building supply chain. With the optimization of the value goals of the relevant supply chain entities as the premise, it explores the coordination and optimization strategies among the relevant entities in the cooperative innovation environment, clarifies the driving factors for cooperative innovation among the relevant entities in the green building supply chain, and constructs an incentive mechanism for cooperative innovation among the relevant entities. It also builds a sustainability evaluation system for green buildings, which is conducive to deepening the research on project incentives, improving the management model of the green building supply chain and project management theory, and providing theoretical support for the innovative development of green buildings. The application of the results can further clarify the responsibilities of each supply chain entity, help resolve the conflicts of interest among different stakeholders in the development of green buildings, thereby achieving the overall goals of green buildings, enhancing their overall value, promoting their sustainable development, and providing policy basis and decision-making references for government departments to accelerate the development of green buildings.