The 19th National Congress of the Communist Party of China has established that socialism with Chinese characteristics has entered a new era. How to strengthen the internal audit supervision in colleges and universities in the new era, this paper starts from the thinking background of strengthening the internal audit supervision in Colleges and universities and analyzes the weak links. It proposes to build a substantial independent internal audit framework, promote the construction of internal audit team on a regular basis, strengthen the audit with science and technology, innovate the internal audit working methods and means, reform the internal audit system with the framework of university governance, and implement audit rectification and strengthen the application of internal audit results from five aspects of rethinking.