The population aggregation and built-up area expansion caused by urbanization can have significant impacts on the supply and distribution of crucial ecosystem services. The correlation between urbanization and ecosystem services has been well-studied, but additional research is needed to better understand the spatiotemporal interactions between ecosystem services and urbanization processes in highly urbanized areas as well as surrounding rural areas. In this paper, the relationships of urbanization with natural habitat and three key regulating ecosystem services—water retention, soil conservation, and carbon sequestration, were quantified and mapped for the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), a rapidly developing urban agglomeration of over 70 million people, for the period of 2000–2018. Our results showed that urbanization caused a general decline in ecosystem services, and urbanization and ecosystem services exhibited a negative spatial correlation. However, this relationship varied along urban-rural gradients and weak decoupling was the overall trend during the course of the study period, indicating a greater need for the protection and improvement of ecosystem services. Our results provide instructive insights for new urbanization planning to maintain regional ecosystem services and sustainable development in the GBA and other large, rapidly urbanized agglomerations.