Abstract: 3D Geological structural model plays a major role in showing the geological information, and has been an essential part of hydrogeology engineering projects. For the lack of borehole data in most regions and the advantages of geophysical technology, this paper takes Hami Basin of Xinjiang where the geophysical data is rich for example, according to the theoretical basis of crusting weathering crust and the change trend of apparent resistivity from geophysical data, the determination method of discrete data inflexion point is applied to classify geological structure, and the classification is verified using drilling hole data; then, to divide the regional geological structure more detailedly, virtual geophysical measurement points are set in deleted regions of geophysical data, and virtual geophysical measurement points are assigned using the distribution of surface quaternary thickness, and according to the layered location of nearby geophysical measurement points; finally, the more accurate 3D geological section model of study area is established using GOCAD. 3D geological section model provides the theoretical basis for further groundwater flow study and water balance calculation, and through showing the modeling process, this paper provides a new idea of regional 3D geological modeling using geophysical data.