This paper employs the structural equation modeling method in the study of the relationship between the knowledge flow and intellectual capital, divides the knowledge flows among enterprises in the supply chain into knowledge exchange and knowledge integration. According to classic classification, intellectual capital is divided into three elements: human capital, structural capital and relational capital. From analyzing the dynamics of intellectual capital, intellectual capital management model, SECI model and organizational learning, four aspects of literature, the article reveals that the process of knowledge flow is the process of intellectual capital management virtually. Through investigation on 237 enterprises, the author used structural equation modeling method to analyze the impact of exchange of knowledge and knowledge integration on the three elements of the core enterprise intellectual capital, of which: there is positive correlation between the exchange of knowledge and human capital as well as relational capital, meanwhile, there is no positive influence between knowledge exchange and structure capital; knowledge integration has positive influence on human capital, structural capital and relational capital. Through living example, it has been elucidating that improving the relationship between knowledge flow and intellectual capital will help enhance the core enterprise intellectual capital.