Taking the non-financial listed companies whose R&D investment in China's A-share market is more than zero from 2007 to 2018 as the research object, this paper empirically studies the impact of R&D investment intensity on financial fraud risk and audit fees, and the effect of CPA audit governance. The results show that the intensity of R&D investment is positively correlated to financial fraud risk and audit fees, and the financial fraud risk has partial mediating effect on the impact of R&D investment intensity on audit fees.In addition, using instrumental variables to make an endogenous analysis, the study finds that R&D investment intensity is very exogenous in the first three measures (R&D investment / total assets, R&D investment / net assets, R&D investment / number of employees), while endogenous in the fourth measure (R&D investment / business income). Through the analysis of the effect of audit governance, it is found that although the high audit fees ensure the high level of CPA practice, the existence of abnormal audit fees positively related to audit collusion indicates that the effect of CPA audit governance is not well.What's more, it is also found that higher abnormal audit fees charged on customers with high R&D investment intensity, customers with high financial fraud risk and high-tech enterprises are usually related to higher audit collusion tendency.