The creation of bay areas is one way to develop economies and culture based on natural characteristics and regional connections; successful examples include the San Francisco, New York and Tokyo Bay Areas. In 2019, China established the Guangdong–Hong Kong–Macau Greater Bay Area (GBA). As a result of historical and geographical factors, the GBA is uniquely characterised by being subject to ‘one country, two systems’, ‘three customs territories’, and ‘three legal systems’. This study offered ample empirical evidence based on qualitative methods referring to in-depth interviews with academics and managers as well as publicly available policies and literature in the GBA. A thematic analysis was used to explore the context and characteristics of developing higher education (HE) in the GBA. The study emphasised that developing GBA’s HE improved its partnerships from co-operation to strategic co-ordination to resource sharing. This research contributes to HE and its governance in the GBA, a topic on which there is limited information in the extant international research literature. It is also useful to policymakers and scholars as it provides potential strategies and insights regarding the development of regional higher education. © The Author(s) 2023.