Regional governance of higher education is one of the important contents in the regional development in the Bay Area, which is composed of Guangdong,Hong Kong and Macao. At present,regional governance of higher education in Bay Area has the characteristics of fragmentation of cooperation attitudes,modes and effects. The reasons for the above characteristics lie in the great differences in the governance modes of the three places and the division in interests caused by the development competition of higher education in the three areas. In order to improve the fragmentation of regional governance of higher education in the area,we need to promote collaborative governance by following the logic of goal establishment from individual to whole,the logic of organizational change from cracking to aggregation,and the logic of action change from division to coordination.