Using the data from the main band listed companies in Shanghai and Shenzhen Stock Exchanges that disclosed separately internal control audit fees and financial statements audit fees from 2011 to 2014, from the perspectives of the features of listed companies, characteristics of accounting firm as well as internal control audit engagement, this paper theoretically analyses and empirically tests the factors influencing audit fees of internal control. It finds that the size of company, the companys business complex level, the state ownership, the accounting firms reputation and the level of assurance of internal control service have a significant positive association with the internal control audit fees, and the quality of internal control, continuous internal control audit period and integrated audit have a significant negative association with the internal control audit fees.