Intellectual capital has important function in value creation and innovation in a company. As to enterprise innovation, the efficient management and reasonable applying of an enterprise' intellectual capital decides the success or failure of the innovation. An enterprise is a live "organism" which has bones, flesh, blood and brain just like an organic "people". We think the three aspects of intellectual capital (human capital, structure capital, and customer or relationship capital) are the most important organic apparatus of an enterprise. In the complicated environment, only when the three aspects operate efficiently like a huge machine, can it make the enterprise innovate and create excess value constantly. So this paper tries to probe into the role of the three aspects of intellectual capital that they act in enterprise innovation using system engineering theory, and it also formulates that enterprise innovation mode based on intellectual capital is: to build instructions and atmosphere which are beneficial for innovation from the inner structure capital optimizing angle; to strengthen the enterprise specific capability of innovator from human capital management angle; to strengthen the value actualization ways of enterprise innovation value from customer or relationship capital management angle.
