The R&D investment has long-term and uncertainty characteristics, the behavior of enterprise's R&D will reduce the current accounting earnings. On the basis of studying the influence of internal control quality on enterprise's R&D intensity, this paper makes a deep analysis on the two ways by means of which the internal control has an effect on enterprise's R&D activity. Namely, controlling the opportunism risk and controlling R&D project operational risk. The results show that the internal control quality is positively related to the intensity of R&D investment. Internal control can significantly restrain the management opportunism risk and R&D project operational risk, which ultimately helps to improve R&D intensity. This paper does not only reveal the internal mechanism of the internal control in R&D investment, but also provides a new empirical evidence for the internal control and the R&D activities of China's listed corporations.