Abstract: Taking G university as an example, it analyzes the status quo and problems of internal control system construction in colleges and universities and found that the main obstacles to the implementation of internal control system in colleges and universities are the rigidity of internal governance structure, the backward mechanism of internal governance risk assessment, weak information construction of internal control system and lack of professionals of internal control system construction. The optimization path of internal control system in colleges and universities based on modern governance can be focused on four aspects: optimizing internal governance structure and improving internal control environment; strengthening the risk management and improving the internal risk control system; promoting the information construction of internal control and improve the technical level of internal control; perfecting the internal control and supervision mechanism and improving modernization governance in colleges and universities.