Within interorganizational cooperative innovation of construction supply chain system, the achievement of project value-adding could be reflected by several factors, such as project-based organizational effect level, and the relationship between project cooperative innovation objectives. In this paper, based on the assumption of equal cooperation between project-based organizations, we selected the knowledge cooperation between the owner and contractor in construction supply chain system as research object. From the perspective of maximizing project value-adding and the relationship of effort cost between knowledge input and innovation stage in consideration, we established the knowledge collaborative incentive model for interorganizational cooperative innovation of construction supply chain system and proposed the first-order and second-order approaches. Then we conducted the digital simulation and example analysis, its results showed that if the owner has the capability to achieve project value-adding in knowledge cooperation, he would adopt a part commissioned way. Otherwise, a fully commissioned way would be better.