Taking Shanghai and Shenzhen A-share listed companies that separately disclosed the internal control audit fees from 2012 to 2016 as the research object, this paper analyzes the influencing factors of the internal control audit fees from the perspective of the supervisory and consultation functions of the board of directors and the board’s discretion in determining the standards for quantitative identification of internal control defects. The empirical results show that the supervisory function of the board of directors and the quantitative identification standard of internal control defects are positively correlated with the audit fees of internal control, and the consultation function of the board of directors is negatively related to the audit fees of internal control. And it also shows that quantitative identification standard of internal control defects has partial mediating effect on the influence of supervisory function of the board of directors on the audit fees of internal control, and it has moderating effect on the influence of consultation function of the board of directors on the internal control audit fee.