Natural disaster is one of the important factors that restrict regional sustainable development. According to disaster system theory, disaster is the result of disaster-causing factors interacting with hazard-formative environment and hazard-affected bodies, but the vulnerability of hazard-affected bodies will aggravate or lighten the disaster to a certain extent. Therefore, the study of disaster vulnerability is important for reducing the risk of natural disaster. The paper takes Xiamen city as an example to analyze the formation mechanism of natural disaster vulnerability from two aspects: natural environment and social-economic system. With the aid of Geographic Information System and Remote Sensing, it obtains detailed geographic data and selects the factors such as natural environment, population, economy, urban morphology, infrastructure to establish the vulnerability assessment indicator system. Then it uses the Weighted Comprehensive Evaluation Method to build assessment model, implements the vulnerability assessment in ArcGIS, and carries out the spatial distribution map of natural disaster vulnerability for Xiamen city. The result shows that the composite index values of natural disaster vulnerability are generally high in Xiamen city, but they vary from district to district while the dominant factors of vulnerability differ a lot. Finally, it points out that the high-value areas of vulnerability should be the focus of anti-natural disaster regions. And according to the dominant factors of vulnerability, each district should take appropriate disaster mitigation measures.