As typical innovation organizations, the structure and efficiency of cooperation among universities’ innovation behaviors are important influencing factors for regional innovation sustainable development. In 2019, the Chinese government promulgated the “Outline of the Development Plan of The Guangdong, Hong Kong and Macao Great Bay Area”, which directly promotes a sustainable cooperation network of universities in the Great Bay Area. This study used UCINET to visualize the cooperation network of universities in Guangdong, Hong Kong, and Macao based on the cooperation data generated by 35 universities in the Guangdong–Hong Kong–Macao Great Bay Area, jointly establishing 37 professional alliances that developed 888 cooperation ties from 2017 to 2022. The results show that the current cooperative network density of universities in the Great Bay Area is high (density = 0.746), but the cohesion trend is not significant (network centralization = 26.92%); a clear circle structure has been formed. The network exhibits a narrow shape at both ends and widens in the middle; the higher the hierarchical position of universities in the region, the more likely they are to enter the core cooperation network and establish more cooperation relationships. Universities in the marginal circles find it especially difficult to initiate cooperative relationships due to their disadvantageous position in terms of limited resources and a lack of administrative intervention. The current cooperation situation still has room for expansion. © 2023 by the authors.