The Fenghuangshan copper mine in Tongling of Anhui province is confronted with a serious shortage of resources, so it is urgent to build the three-dimensional structure models of geologic bodies, analyze ore-controlling geological factors and then make stereotactic and localization prognosis on deep concealed ore bodies. The localization of Fenghuangshan ore deposits and ore bodies is mainly in the compound control of the contact zone and the fault structures, where the Xinwuli magmatic body is intrusively in contact with the surrounding rocks, parts of the zone overlap on surrounding rocks, and the shape and occurrence of the contact zone controls the spatial distribution of ore bodies. Based on analyzing the ore field’s geological characteristics and mineralization, the 3D structure raster models of the Xinwuli magmatic body, the contact zone, strata and tensional faults were built by using the 3D geological modeling technology. The 3D structure models of geologic bodies show that the structure of Xinwuli magmatic body is complex, extending to the southeast, having a lot of severe bending, and being fanned in the northeast; the contact zone of the magmatic body and the surrounding rocks controls the occurrence and spatial distribution of ore bodies; the structure of strata is a compound syncline; and the fault structures are four transverse tensional faults stretching northwest. Based on the raster models, combining mathematical morphology with Euclidean distance transformation, the structure of the Xinwuli magmatic body were filtered, decomposed and analyzed geometrically, and then the 2 levels trend components and the 2 levels undulate components of the magmatic body were acquired. The 3D raster models of the thermal field factor (dG), the morphological factors (wr1G and wr2G), the fold structure factor (dD3) and the transverse tensional fault factor (dF) were built by the spatial analysis method and used to express the mineralization enrichment space and its stereoscopic units by means of making scatter diagrams and statistic analysis to get the relation between the ore-controlling geological factors and the mineralization indicators. The raster models of geologic bodies and ore-controlling geological factors could describe the distribution of geologic bodies and ore-controlling geological process in space, analyze the relationship among 3D structure of geologic bodies, ore-controlling geological factors and spatial distribution of mineralization, and provide the spatial analysis and 3D visualization models for stereoscopic prognosis on deep concealed ore bodies.