Under the background of national strategy and policy, the key to support Guangdong-Hong Kong-Macao Greater Bay Area (GBA)’s construction is the main role of active governance of colleges and universities. How to play the main role and promote the governance of colleges and universities in GBA has gained extensive attention. For catching up on the missing of the evaluation system of university collaborative governance degree in GBA and promote the improvement of university collaborative governance in GBA, this paper puts forward a new university collaborative governance path model in GBA, and establishes a relatively perfect evaluation system framework of university collaborative governance degree in GBA. By collecting a large number of 2754 questionnaires in GBA, Then the Analytic Hierarchy Process (AHP) is used to determine the weight of each level index of the collaborative governance degree of colleges and universities in GBA. According to the data, the Fuzzy Comprehensive Evaluation method (FCE) is used to evaluate the current collaborative governance degree of colleges and universities in GBA. Finally, detailed improvement suggestions are given on the weak links. Based on the evaluation results, this paper concludes that the improvement order of the current collaborative governance degree of universities in GBA is the collaboration between the government and universities, the market and universities, the internal collaboration between universities, and the society and universities, We should focus on optimizing the power of the Development Advisory Committee of colleges and universities and promoting the innovation of higher education system and mechanism in an all-round way. Using this method, we can accurately evaluate the current situation of university collaborative governance in GBA from both qualitative and quantitative aspects, and provide a scientific basis for improving the degree of university collaborative governance in GBA.