With China’s urbanization advancing into an advanced phase, urban clusters experiencing swift expansion of urban land have emerged as “disaster areas” where ecological environment problems are highly concentrated. Therefore, paying attention to the habitat quality of urban agglomerations and their ecological cooling effect is crucial for improving the quality of the living environment and fostering sustainable development in the region. This research uses the Guangdong-Hong Kong-Macao Greater Bay Area (GHM-GBA) as a case study, applies the InVEST platform, Geographic Information System (GIS), and Binary Moran’s I index, and undertakes an investigation into the spatial interplay between the habitat quality pattern and the thermal environment within the urban clusters of the GHM-GBA between 2000 and 2020. Firstly, utilizing data on habitat threat density, the Habitat Quality Module on the InVEST platform is employed to measure the habitat quality and degradation extent of urban agglomerations. Secondly, based on MODIS satellite sensor data, the surface temperature is inverted and interpreted, and the spatial heterogeneity traits of the urban agglomeration’s thermal environment are examined. Then, the Binary Moran’s I index is used to clarify the spatial clustering and spatial dispersion relationship characteristics between habitat quality and thermal environment, including the network spatial distribution of regions with positive spatial correlation and negative spatial correlation. Ultimately, through the lens of urban design, this paper puts forward detailed planning recommendations to improve the quality of living spaces and thermal comfort within urban clusters. These suggestions serve as a reflection for the ecological sustainability, livability, and high-quality growth of the GHM-GBA.