A total number of 65 samples from 13 drill holes from the Perama Hill epithermal Au deposit were analyzed by X-ray diffraction, Scanning Electron Microscopy, and Transmitted and Reflected Light Microscopy. The major lithologies and the four identified hydrothermal alteration zones, including an Argillic to Advanced Argillic alteration zone, an Argillic alteration zone, a Silicification zone, and an Intermediate Silicic-Argillic alteration zone, were imported in the Geovia SURPACT software and 3D models of host rock lithology and hydrothermal alteration zoning of the deposit were modeled. The models show that the most intense hydrothermal alteration phenomena occurred at the central and southern part of the Perama Hill deposit. At the central part, a large depression is present indicating the pathways of the main feeder zones which are closely associated to the Advance Argillic to Argillic hydrothermal alteration and Silicification zones with evidence of overprinting between the two. The 3D modeling also showed a sudden spatial dispersion of the hydrothermal alteration zones (Argillic alteration) at the transition between the lower cohesive andesitic breccia and the overlying unconsolidated and highly porous felsic volcanic sandstone. The precious and critical metal content of the deposit is rapidly increased at the intermediate conglomerate, indicating that the sudden change in host rock hydraulic conductivity played a major role in the formation of the Perama Hill Au deposit.