Abstract: Based on the theoretical studies of national innovation system, national innovation (system) governance system and national innovation (system) capability, this study first constructs three evaluation systems for the development level of national innovation governance system, national innovation capacity and the adaptability between the both; secondly, measures the development level of innovation governance system in China and OECD countries by using entropy value method, mean squared difference method subjective evaluation G1 method and fuzzy Borda method; again, adopts LightGBM machine learning is used to identify the key elements of the governance system driving national innovation capacity enhancement; finally, gray correlation is used to explore the overall adaptability of governance system and innovation capacity. It is found that: firstly, the level of development of innovation governance systems varies significantly across countries, and uneven development of the dimensions of governance systems reduces the level of governance; the uneven development of each dimension of governance system will reduce the level of governance; China is a low level country; improving policy tools and institutional rules will help to improve the development level of governance system. Second, the ratio of government R&D funding allocation, the number of policies, and the proportion of R&D talents in the whole society are the three key factors of the national innovation governance system driving the improvement of national innovation capacity. Third, when the level of national innovation governance system and national innovation capability are comparable, both show adaptability, and China belongs to high adaptability, and the high reason is the roughly homogeneous development of innovation governance system and national innovation capability. The research results help to improve the national innovation governance system and enhance the national innovation capacity, and provide a basis for decision-making on the reform of the national science and technology innovation system and mechanism to make up for the shortcomings.