Health, safety and well-being of human society are closely related to ecosystem health. In the context of global climate change, natural disasters occur frequently. The comprehensive effects of various natural disasters have caused significant negative impacts on the global ecological environment. As a study case, the tropical cyclone, rainstorm waterlogging and geological disaster in Guangdong Province of China were selected as the risk sources, and the regional ecological risk of the three natural disasters was comprehensively assessed in this area. As a prerequisite for the risk assessment, this paper focused on the hazard assessment of tropical cyclone, rainstorm waterlogging and geological disaster and their comprehensive hazard. With the support of GIS technique, by the grid of 1 km*1 km as the basic evaluation unit, the zone map of comprehensive hazard of the three natural disasters was obtained. The results indicate that the hazards of tropical cyclone and rainstorm waterlogging decrease from the coast to the inland, and their high hazard zones are concentrated in southwestern coastal areas, while the high hazard zones of geological disaster are mainly distributed in the inland hilly areas of the northeast and west of the province, as well as, the comprehensive hazard grade also decreases from southeastern coast to northwestern inland, displaying an irregular strip distribution around the coastal shoreline. There are some differences in the spatial pattern of the hazards of the three natural disasters, but they are linked each other and exist a relationship of cause and effect, and their combination may result in forthcoming serious disasters. The results of hazard assessment are the basis of ecological risk assessment, and the comprehensive evaluation of various natural disaster risks is proved to be an effective way to mitigate the natural disaster for Guangdong Province.