Abstract:The National Key R&D Programs (NKPs) are an important measure for China to implement the innovation-driven development strategy. In order to comprehensively and deeply understand the internal mechanism of innovation governance of NKPs and effectively improve the efficiency and effectiveness of innovation governance, this study proposes a "Super-helix Model" supported by case study analysis of 11 key projects of the NKPs and referred to the DNA molecular helix structure. The model includes two core chains, namely, the industrial chain and the university research chain. Through the four docking bases of talent, capital and equipment, knowledge and information, and value interests, the connection keys are formed according to certain rules. The force field created by the government's science and technology policies and industrial policies is the central direction axis to lead the two core chains. Based on this model, the research analyzed the influencing factors and mechanisms of achievements transformation of NKPs from the four dimensions of core scientific research personnel, team technical ability, team comprehensive strength, and external policy environment, and analyzed the corresponding management countermeasures from four development stages.