Through statistical analysis of reports from news media in Guangdong, Hong Kong, and Macao on ecological environment cooperation in the Guangdong-Hong Kong-Macao Greater Bay Area, as well as comparative text analysis of ecological environment regulation of Guangdong, Hong Kong, and Macao, this paper reviewed the process of collaborative ecological environment governance in the Greater Bay Area, and discovered its characteristics, deficiencies and restrictive factors. Then it established a framework to explore the approaches of further collaborative governance in the study area. It is found that the collaborative ecological environment governance in the Greater Bay Area had been increasing during 2000-2019. The collaborative governance between Guangdong and Hong Kong, or among cites in the Pearl River Delta contributed a lot, but there was less regional collaborative governance covering Guangdong, Hong Kong, and Macao. Holding conferences and signing related documents were the major means of collaborative governance in the area, but there were few practical actions due to the lack of operability. Most of the collaborative governance focused on the protection and renovation of water and atmosphere environment, but the diversity of cooperation fields was insufficient. At the same time, the patterns of environmental governance of Guangdong, Hong Kong, and Macao are quite different. In the process of environmental governance, the three areas are not identical in terms of subject of liability and enforcement, object of regulation, approaches and intensity of governance, contents and standards of regulation, as well as scope of supervision, which have become constraints on collaborative ecological environment governance in the region. Based on the above findings, the paper suggested that the collaborative ecological environment governance in the Guangdong-Hong Kong-Macao Greater Bay Area should be promoted to more comprehensive scales, more effective forms and more diverse fields. Firstly, the collaborative ecological environment governance in the region should be stimulated from a more comprehensive scale, to promote the interconnection of the whole region. Moreover, it is necessary to combine multiple forms of governance to improve the operability of collaborative governance. Finally, besides water and atmosphere protection and renovation, the fields of collaborative ecological environment governance should be expanded to promote broder cooperation.