Enterprise innovation needs financial support, currently, bank credit is still the main financing channel for China’s enterprise innovation. Because the credit decision-making of the commercial banks usually has higher risk evasion preference, the innovative activities of the enterprises always have the characteristics of high risk and long cycle, which cause that the growth of bank loan scale of the enterprises is possible to restrain their innovative activities, among which long-term loan is not conducive to enterprise innovation, but the increase of short-term loan is helpful to enterprise innovation. Meanwhile, the narrowing of the net interest margin of the banks reduces the short-term financing cost and is further conducive to the increase of enterprise innovation input. The interest rate marketization enhances the pricing right of the loan of the commercial banks and inter-bank competition, makes the banks increase the opportunities and motive for obtaining risk premium price, further changes banks’ credit decision-making and possibly has two-sided impact on enterprise innovation effect of banks’ credit. The banks increase the loan for enterprise innovation items （especially long-term loan）, weakening the restraining effect of loan scale increase and long-term loan growth on enterprise innovation. The banks strengthen the adjustment of the loan interest rate for enterprise innovation items （especially short-term loan）, weakening the promotion effect of the net interest margin of deposit and loan of the banks and the increase of short-term loan on enterprise innovation. The analysis of the data of A-share non-financial listed companies in Shanghai and Shenzhen from 2008 to 2017 shows that interest rate marketization as a whole promotes R&D activities of the enterprises but is “a double-edged sword” to affect enterprise innovation through bank credit, on the one hand, weakening the restraining effect of loan scale increase and long-term loan growth on the input and output of the enterprises’ R&D activities, on the other hand, weakening the promotion effect of loan interest rate reduction and short-term loan increase on the input and output of the enterprises’ R&D activities. Further analysis finds that the enterprises with different ownership, industries and scales have the heterogeneity for the impact of interest rate marketization on their innovation activities through bank credit and that five state-owned commercial banks and other stock commercial banks have different performances in this process. We should actively boost interest rate marketization reform, continuously perfect the financial market mechanism for fair competition, let policy-bank play the support role, further consolidate the policy support for medium-sized and small banks and medium-sized and small enterprises, improve the innovative item preference of commercial bank credit decision-making so as to effectively reduce the financing cost of enterprise innovation to boost the input and output growth of enterprise innovation.