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Establishing an appropriate and visual 3D query system of flood submerging could reflect extent of flood disaster directly, it is very important for the sectors of flood-control and disaster-relief, which they can determine disaster-relief target and planning. Due to problems with application of GIS on flood-control and disaster-relief, based on the topographic map of Fuzhou city, we established related database of flood submerging, and developed a 3D model of flood submerging using Visual C++ developing language and ArcEngine component library. This text gives a detailed introduction on generation of 3D terrain; query of terrain elevation, display of water line, flood submerging area, economy appendage, achieving process of statistics on pecuniary loss in flood submerging area, and so on. Intuitive and 3D visual effects reflected the spatial distribution situation of flood, overcoming the defects of traditional 2D GIS, laying the foundation for the rational decision-making in flood-control and disaster-relief.