This work aims at figuring out the spatial relationships between the geophysical and geological models in a case study pertaining to copper-sulfide mineralization through an integrated 3D analysis of favorable target. The Ghalandar Skarn-Porphyry Cu Deposit, which is located in NW Iran, is selected for this research work. Three geophysical surveys of direct current electrical resistivity and induced polarization tomography along with magnetometry are performed to construct the physical properties of electrical resistivity, chargeability, and magnetic susceptibility, respectively. Inverse modeling and geostatistical interpolation are utilized to generate the physical 3D models. A 3D model of Cu grade is generated using ordinary kriging; however, the indicator kriging method is run to design a 3D model of rock types through incorporating the drilling results. Block models of geophysical and geological characteristics are cast in a similar 3D mesh to investigate their relationships in copper mineralization. A concentration-volume multi-fractal method is utilized to divide each model into its sub-sets, where the most productive portions in association with Cu-bearing mineralization are distinguished. Note that sub-sets of geophysical models are spatially matched with geological models of Cu grade and rock types. The zones with low electrical resistivity, high chargeability, and low magnetic susceptibility correspond to the main source of Cu mineralization in a dominated skarn rock type setting.