In-depth research on the spatial and temporal evolution of ecosystem service trade-offs and synergistic relationships, scientific identification of ecosystem service bundles, and the main factors affecting the spatial differentiation of ecosystem service bundle provisioning are crucial to enhancing the overall benefits of regional ecosystem services and human well-being. Based on the assessment of the Guangdong–Hong Kong–Macao Greater Bay Area ecosystem service functional system, we combined the correlation analysis method, hierarchical clustering method, and principal component analysis to analyze the trade-offs/synergistic relationships of 11 indicators contained in four major ecosystem service categories of the Guangdong–Hong Kong–Macao Greater Bay Area and explored the study of ecosystem service bundle identification and clustering spatial differentiation. The results of this study showed the following: (1) Between 2000 and 2018, Regulating and Supporting services showed a decreasing trend while provisioning and cultural services showed an increasing trend. Human interference affected the spatial differentiation of ecosystem services provision; the provision of individual ecosystem services was more random, but the geospatial distribution showed a certain degree of regularity. (2) The intrinsic connection of ecosystem services is continuously strengthened, and the other four ecosystem services except industrial products in the provisioning services easily produce synergistic relationships with regulating and supporting services, while industrial products, leisure and recreation, scientific research and education, and other ecosystem services are more likely to produce a trade-off relationship between them. The correspondence among ecosystem service trade-offs, synergistic relationships, and cold/hot spots is not uniform due to spatial scales. (3) The method of combining socio-economic statistics and the InVEST model can identify similar ecosystem service bundle classifications, but there are differences in the performance of some of the roles at different study scales and in different study areas. (4) For complex urban-natural ecosystem services, the classified ecosystem service bundles have broad similarities. The development of high-density city clusters depends on the coordinated development of the population, resources, environment, society, and economy of each city in the region.