Abstract: With the country’s emphasis on the development of colleges and universities,the increasing funding and scale of running colleges and universities,the Ministry of Education and the Ministry of Finance put forward higher requirements for the construction of internal control in colleges and universities,the key to improving the quality of internal control lies in whether the evaluation of the internal control system is scientific and reasonable.This paper made an in-depth analysis of existing problems,the construction of the internal control operation evaluation index system of colleges and universities from the current situation of internal control evaluation as the starting point.It put forward countermeasures and suggestions to improve the internal control operation evaluation system of colleges and universities.