The rising sea levels caused by global climate change and rapid urbanization will have a significant impact on the distribution and landscape patterns of coastal habitats. Assessing the vulnerability of coastal wetlands under the influence of sea level rise is an important basis for ecological restoration and management of the regional environment. Taking the Guangdong-Hong Kong-Macao Greater Bay Area as an example, this study used the SLAMM model and Fragstas model to predict and analyze the changes in area, distribution, and vulnerability of mangroves, salt marshes, and tidal flats under six scenarios of sea level rise and land use coupling by the year 2100. The results showed that: 1) With the rising sea levels, mangroves and tidal flats are experiencing severe degradation. The high vulnerability zones of mangroves are mainly distributed in the estuaries of the Xi Jiang River, Zhu Jiang River, and the east coast of the Huang Mao Sea. The high vulnerability zones of tidal flats are evenly distributed along the coastal areas of the Greater Bay Area. In comparison, salt marsh habitats are less affected by sea level rise. 2) Compared to mangroves and tidal flats, land use patterns have the most significant impact on salt marsh habitats. Under the scenario of protecting the developed land, the salt marsh area in the western part of the Zhu Jiang River estuary significantly increases with low vulnerability. Under the scenario of protecting all upland areas, although the salt marsh habitat area is maintained, the landscape pattern is severely disrupted, resulting in high vulnerability. The study suggests dynamically adjusting land use strategies for high-vulnerability areas, clearing space for coastal wetlands to migrate inland, and enhancing the adaptability of coastal habitats to sea level rise. The findings can provide scientific support for the management and protection of coastal wetlands.