The rapid development of the web geographic information system (Web GIS) has promoted new vitality in high school geography education, relieved the stress of geography teachers caused by software and technical problems, and made it possible for teachers to devote more energy to geography teaching and research activities. Natural disaster education is not only an important part of the geography curriculum, but also an indispensable aspect of education for sustainable development (ESD) for high school students. The application of Web GIS in the dynamic monitoring, forecast, and early warning of natural disasters is becoming more experienced. Therefore, the application of Web GIS in natural disaster education is quite feasible. How to build a bridge between them is the purpose of this paper. Thus, the paper selects ArcGIS Online, which is not limited by time and space, and analyzes several functions that apply it to geography teaching. These include smart mapping, story maps, 3D web maps, and mobile GIS. Meanwhile, it analyzes the knowledge structure of “natural disasters” in Chinese geography textbooks to guide the subsequent case design. Then, the Web GIS inquiry-based teaching case is formed based on “7.20 Zhengzhou Torrential Rain”. It contains knowledge about natural disasters and designs from many aspects, such as the causes, manifestations, and prevention and control of disasters. The discussion identifies a range of specific educational benefits of applying Web GIS to natural disaster education for teachers and schools. Ultimately, it can provide some reference values for geography teachers and other developers to explore curriculum resources and create quality educational models.