Internal audit in colleges and universities as the "immune system" of colleges and universities, plays an important function of "immune". This article will discuss how to effectively play the prevention function, the stabilizing function, monitoring function of internal audit in colleges and universities from two aspects about the setting of the internal audit institutions and innovation of the audit content, and points out that colleges and universities should reform setting form of the internal audit institutions and internal audit personnel appointment system, and explore how the internal audit institutions in colleges and universities carry out the budget planning audit, performance audit on the basis of the traditional audit content, and vigorously promote the whole -process follow-up audit about major construction project, to maximize the prevention of corruption, waste and other problems, ensure the healthy and orderly operation.