To achieve self-reliance in high-level science and technology and improve the financial support for national innovation system is a key policy. On the basis of sorting out the theoretical origins of the national innovation system of financial support, based on the basic principles of the national innovation system and comparative finance, this paper makes a comparative analysis of the national innovation system of financial support in China and the United States from the perspective of demand and supply. It is found that the United States is in the mature stage of its innovation system, while China is in the growth stage of its innovation system. The financial system of the United States is more market-oriented, while the financial system of China is more bank-oriented, but it is transitioning to market-oriented, and the financial supply is undergoing new changes. China and the US innovation systems and financial support innovation systems have different weaknesses and different missions, but they face the common challenge of achieving high-quality development in the period of technology-economic diffusion. On the basis of the above conclusions, it insists on the unification of the question guidance and the objective guidance, and put forward the enlightenment suggestions to perfect our country’s science and technology finance system.