Over the past few years, the change rate of business environment has accelerated and the nature of change is also essentially different. The competitive advantage of the product is not only focus on cheaper product and faster delivery, but also use a more flexible and open approach to face the whole new challenges. At this time, efficient and innovative value chain management has become an important start. Therefore, value chain management and its continuous innovation is an important start. Based on the needs of their survival and best practices of the successful enterprises, prompting increasingly focusing on value chain management, and actively perform change and reengineering the value chain in accordance with the changing business management environment, in order to enhance the competitiveness of enterprises. Facing such increasingly competitive environment, the enterprise value chain management requires a systematic innovation system.In this paper, we refer the innovation radar diagram proposed by the professor Mohanbir Sawhney to explore the impact and relevance of the innovation system for value chain management. First, we establish the innovation system performance assessment index system including four dimensions and 12 criteria through related literature review. Secondly, DEMATEL method is applied to construct the innovation system performance evaluation model for value chain management, which reflects the impact and relevance among these innovation performance evaluation criteria. Then, DANP is used to calculate relative influence weight of these innovation performance assessment criteria. Finally, we used VIKOR to evaluate the innovation system performance of one company for case study to find out the worst innovation performance index. Consequently, we suggest some specific improvement strategies and action items for the company based the proposed value chain innovation system model.