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The paper takes Yinchuan plain as a research object, and basically investigated the quaternary geology and the spatial distribution and structure characteristics of groundwater system. The method of virtualizing boreholes is used to increase borehole data in accordance with the well-developed geological structures, the complex strata and lithology, the multiple geomorphologic units, the large area and the unevenly distributed boreholes. Based on the platform of geostatistics and Groundwater Modeling System (GMS), the three-dimensional geological structure model has been set up which reflects the hydrogeological conditions in the study area and the visualization of hydrogeological structure has been realized. All of these provide the foundation for exactly evaluating groundwater aquifer and rationally developing and utilizing groundwater.