Coastal wetlands are one of our most valuable ecosystems; they have high biodiversity and productivity. In recent years, with the development of urbanization and the acceleration of industry progress, the land use in China has undergone some prominent and profound changes, and the ecological risk is becoming increasingly obvious. Here, using original Landsat TM/ETM+ and Landsat 8 OLI satellite images from the years 2000, 2005, 2010, and 2015, and merging administrative and topographic maps, we introduce a model which assesses the risk of multiple marine and coastal utilization projects to habitats, called the Habitat Risk Assessment (HRA) model. We use this model to reflect the current ecosystem risk in the South Fujian Golden Delta so that managers of the area can take adaptive measures. The results show that (1) overall, the risk to tidal flat wetland in the coastal South Fujian Golden Delta is mainly low; (2) the risk area in Quanzhou is the largest (about 4389.91 hm²) while the risk area in Zhangzhou is the smallest (about 4630.73 hm²); (3) after correcting for the influence of each land-use type's area, other construction land has the greatest exposure and consequence to coastal tidal wetlands, whereas plantation has the least exposure and consequence. The visualization of tidal flat wetland risk in different areas enables us to monitor high risk areas, and determine factors that cause high risk areas. Thus, it is more convenient for managers to take adaptive conservation measures.