China’s economic growth drivers is in the bottleneck stage of conversion to innovation-driven, serving the main body of science and technology innovation financing is the core strategic positioning of the capital market, but a long time the proportion of the high proportion of traditional enterprises squeezed the financing space. This paper extends Schumpeter’s endogenous growth model and theoretically analyzes how the structure of capital market financing main body affects the innovation activities and total factor productivity of this economy. Based on the OECD high-tech industry classification methodology, global listed companies are categorized into traditional firms (low-tech industries) and high-tech firms (high-tech and emerging industries), and empirical tests are conducted using cross-country panel data. It is found that increasing the proportion of high-tech enterprises financing in the capital market can significantly promote the country’s TFP growth, and its mechanism of action is to promote the overall R&D level of high-tech enterprises, and the R&D of high-tech enterprises can bring about more obvious TFP growth compared with the R&D of traditional enterprises. Further analysis shows that when the economy is in the early stage of development, adjusting the structure of capital market financing entities cannot bring significant TFP growth, and optimizing the structure of financing entities to promote TFP growth requires the economy to reach a certain stage of economic development. In addition, the higher the degree of independent innovation, the stronger the TFP growth effect of adjusting the main structure of financing. China should optimize the structure of capital market financing bodies and further tilt resources to emerging industries to meet the financing needs of developing new quality productivity.