The super‐deduction of research and development (R&D) expenses is at the core of the policy to stimulate enterprise innovation in China. This paper identifies whether firms are supported by the super‐deduction policies for R&D expenses and uses the difference‐in‐differences method to investigate the impact of the policies on R&D investment. The results show that changes in policy in 2013 significantly increased the R&D investment of firms engaging in key state‐supported technologies. Policy changes in 2016 significantly increased the R&D investment of firms engaging in non‐key‐state‐supported technologies. Enterprises not only invested all their tax incentives in R&D activities but also increased their investment in self‐raised funds. The super‐deduction policy had different impacts on different industries, firms with different boards, and firms with different ownership. The policy significantly affected the manufacturing and construction industries, the Small and Medium Enterprise Board, and non‐state‐owned enterprises. Through a mechanism analysis, we found that the policy significantly reduced the user cost of R&D and increased the net cash flow of enterprises, which could raise a firm's R&D investment. It is necessary to increase policy support, expand the scope of super‐deductible expenses, and increase the super‐deduction rate based on industry classification according to the sensitivity of different industries to the policy.