Innovation is the driving force behind enterprise development. Improving the quality of the internal control of enterprises and increasing the intensity of R&D investment are important ways to enhance the level of scientific and technological innovation. Based on the data of Shanghai and Shenzhen A-share listed companies from 2010 to 2019, in this paper, we empirically examine the correlation between the quality of internal control and the intensity of R&D investment by using the level of corporate cash holdings as an intermediary variable. We find that high internal control quality can improve cash-holding level and that improving cash-holding level will increase R&D investment intensity. That is, cash-holding level has a mediating effect between internal control quality and R&D investment intensity, while internal control quality can have a direct or indirect positive effect on R&D investment. Accordingly, this study has important theoretical significance and practical value for enterprises that seek to promote R&D innovation and improve their internal control.