National Innovation System plays an important role in the national economic capabilities and competitiveness. Based on the theory of National Innovation System,this paper points that the failure system leads to the low innovational performance,so the government intervention on the S&T innovation should consider on not only the failure of market, but also the failure of system.From the viewpoint of this,the National R&D Program plays an important role in building National Innovation System and repairing the system failure.It analyses the contribution of two important R&D programs in the world and the role of Chinese High-tech R&D (863) Program in building the National Innovation System and suggests making an evaluation to exert the role.