In this paper, we aim to present a quantitative modeling for delineating the alteration zones and lithological units in the hypogene zone of Masjed-Daghi Cu-Au porphyry deposit (NW Iran) based on the drill core data. The main goal of this work is to apply Ordinary Kriging (OK) and concentration-volume (C-V) fractal model based on Cu grades in order to separate the different alteration zones and lithological units. Initially, anisotropy was investigated and modeled based on calculating the experimental semi-variograms of the Cu values, and the main variography directions were identified and evaluated. Then a block model of the Cu grades was generated using the kriging, and the estimation obtained for OK was applied to the C-V fractal model. The C–V log–log plot based on the estimation method represents the various alteration and lithological zones via threshold values. The comparison and interpretation of the alteration zones and lithological units based on the C–V fractal modeling proved that the method was acceptable and capable of correctly delineating the alteration and lithological units. Regarding the correlation derived from log ratio matrix (used to compare the geological model with the C-V fractal results), it was observed that Cu values less than 0.4% were obtained for OK overlapped voxels with the phyllic alteration zone by an overall accuracy (OA) of 0.737. The spatial correlation between the potassic alteration zones resulting from a 3D geological modeling and the high concentration zones in the C-V fractal model based on OK indicated that the alteration zone contained Cu values greater than 0.4% with OA of 0.791. Also using this method, trustworthy results were obtained for the rock units.