Abstract:With?the ever-changing innovation environment and the increasingly frequent interactions between innovation entities, cooperative innovation in the Bay Area has gradually become a hot topic of concern. However, the cooperative innovation of the Bay Area?in China?is still at the initial stage of exploration, and its cooperative innovation mode needs to be developed. Using social network analysis methods, the study selects 20 universities in the urban agglomeration of the Guangdong-Hong Kong-Macao Greater Bay Area as the objects of investigation. Taking the HowNet database as a retrieval platform, the research analyzes the innovation level of scientific research cooperation among universities and understood the basic situation of their scientific research cooperative innovation. The study found that the frequency of cooperation among 20 universities in the Guangdong-Hong Kong-Macao Greater Bay Area is relatively low, the motivation for cooperation among the universities in Hong Kong and Macao is generally insufficient, and the degree of participation of the universities in Hong Kong and Macao is lower. The cooperation among inland universities is dominant and the frequency of cooperation depends on relevant policies and disciplinary advantages. The cooperation mode is mainly through research projects and academic exchanges; the innovation mode of scientific research cooperation presents a new mode of strong cooperation and cross-regional cooperation. In addition, in order to promote the innovation of scientific research cooperation among universities in the Guangdong-Hong Kong-Macao Greater Bay Area urban agglomeration and improve its spatial cooperation mode, it is proposed to break through the restrictions of geographical barriers, carry out multi-level cooperation dimensions, coordinate cross-regional disciplinary cooperation, and enhance the cluster development of cooperation and innovation in the Bay Area by relying on research projects.