This study starts with the architecture design of the internal audit effectiveness measurement index system, taking internal audit effectiveness as the measurement target, from the three dimensions of audit performance, audit capability, and audit "three systems" effectiveness to build a set of 10 components and 30 measure indexes indicator system for internal audit effectiveness measurement. And we take the internal audit of colleges and universities as the research sample, and make an empirical analysis of the built-up internal audit effectiveness measurement index system using the AHP-Fuzzy method to measure the model. We found that the existing problems of internal audit effectiveness are mainly reflected in the obstacles of the audit management system, large losses and waste, ineffective audit rectification and lagging audit innovation. Based on this result, China should take the reform of the internal audit management system as a breakthrough point, promote full internal audit coverage, increase audit supervision and rectification, improve audit innovation capabilities, and establish an internal audit effectiveness measurement index system to strengthen the internal audit effectiveness management responsibility system.