Based on the data of A share listed companies in Shanghai and Shenzhen stock exchanges from 2014 to 2019, this paper discusses the impact of enterprise innovation on abnormal audit fees. The empirical results show that the higher the innovation investment, the higher the abnormal audit fees. Further research shows that the increase of innovation investment would induce real earnings management, which will lead to the increase of abnormal audit fees; The heterogeneity test shows that the legal environment and size of accounting firms are the important moderating factors of the impact of enterprise innovation on abnormal audit fees. In the samples of better legal environment and non international “Big Four” audit, the impact of enterprise innovation on abnormal audit fees is more significant. The results provide an empirical basis for auditors and relevant departments to strengthen the audit and supervision of R&D activities.