The experimental instruments and equipment fixed assets of colleges and universities are the crucial supporting conditions and material foundation guarantees for the development of higher education. How to evaluate the performance of internal control management of experimental instruments and equipment scientifically and effectively is of great practical significance for improving the level of internal control management of experimental instruments and equipment. In this paper, the five elements of the COSO internal control integrated framework theory were embedded in the experimental instruments and equipment management of colleges and universities. The performance evaluation index system of internal control of experimental instruments and equipment management in colleges and universities and the performance evaluation model of internal control of experimental instruments and equipment management in colleges and universities based on fuzzy comprehensive evaluation were constructed, and an example of a university was given to make an empirical analysis. The analysis shows that using the model of experimental instruments and equipment management performance evaluation of internal control can objectively and quantitatively reflect the level of performance management of the internal control of experimental instruments and equipment in colleges and universities, and promote the standardized management and internal control performance management of experimental instruments and equipment in colleges and universities.