Based on the sample of Chinese public listed companies from 2009 to 2012, using the hierarchical regression model, this study examines the relationship between the corporate income tax and its R&D expenditure, analyzes the moderating role of capital structure on the relationship of them, and further examines the influence of different property rights. The results show that there is a negative relationship between the income tax and the R&D expenditure, and because of the impact of debt tax shield, the capital structure could relieve the constraints of tax burden on R&D expenditure. And the moderating effect of capital structure is more significant on non-state-owned corporations. This study makes a breakthrough of separately analyzing the relationship between R&D expenditure and income tax or capital structure, which may provide new evidence for the decisions of R&D investment and the choice of capital structure.