Based on the panel data of listed companies in information technology industry from 2014 to 2018, this paper studies the relationship between government subsidy and R&D Investment of information technology enterprises by using item-by-item regression method. Taking capital structure as an adjusting variable, this paper discusses the moderating effect of capital structure on the relationship between government subsidy and R&D Investment, and further analyzes the difference of the relationship among capital, government subsidy and R&D investment in different ownership enterprises. The results show that the government subsidy has a significant positive effect on the R&D investment of IT enterprises, and the capital structure has a negative correlation with the R&D investment. Capital structure has a negative moderating effect on the relationship between government subsidy and R&D investment, and non-state-owned enterprises are more significant than state-owned enterprises. Therefore, information technology enterprises should improve their capital structure, borrow in a reasonable way, improve profitability, and reserve sufficient funds for R&D activities. The government should increase subsidies for R&D investment in information technology enterprises, especially non-state-owned enterprises, and provide financial and policy support.