Coastal habitat dynamics and ecosystem function in response to human-induced disturbance, especially urbanization, are of increasing concern. However, how changes in landscape composition as well as habitat quantity and quality may affect the long-term sustainability of rapidly urbanizing coasts remains unclear. This study aimed to quantify the extent, change rate, patterns, change process and interrelationships of mangrove habitats, impervious surfaces, and other land cover types in Deep Bay in the Guangdong-Hong Kong-Macau Greater Bay Area (GBA), China, the world’s largest megalopolis, from 1924 to 2020. We processed historical aerial photos (1924–2020) and multiple sources of satellite data (1973–2020) for different types of land cover mapping. Post-classification analysis, including correlation analysis and change detection analysis, was conducted based on the long time-series land cover classification results. Mangrove habitats increased in Deep Bay from 1924 to 2020, except for a large area decrease from 1954 to 1964 due to the construction of tidal aquaculture ponds. Mudflat areas contributed most to the expansion of mangrove habitats of about 275 ha from 1987 to 2020. During this period, reclamation and urbanization for the construction of the megacity of Shenzhen turned large areas of water and mudflat (about 4000 ha) on the northern shore into impervious surface and urban vegetation. Overall, the landscape pattern of mangrove habitats in Deep Bay showed increasing connectivity and decreasing degree of fragmentation from 1987 to 2020. These changes have significant implications for the ecosystem services, e.g., supporting migratory waterbirds, supported by these wetlands.