Three-dimensional geochemical modeling of ore-forming elements is crucial for predicting deep mineralization. This approach provides key information for the quantitative prediction of deep mineral localization, three-dimensional fine interpolation, analysis of spatial distribution patterns, and extraction of quantitative mineral-seeking markers. The Yechangping molybdenum (Mo) deposit is a significant and extensive porphyry-skarn deposit in the East Qinling–Dabie Mo polymetallic metallogenic belt at the southern margin of the North China Block. Abundant borehole data on ore-forming elements underpin deep geochemical predictions. The methodology includes the following steps: (1) Three-dimensional geological modeling of the deposit was established. (2) Correlation, cluster, and factor analyses post delineation of mineralization stages and determination of mineral generation sequence to identify (Cu, Pb, Zn, Ag) and (Mo, W, mfe) assemblages. (3) A three-dimensional geochemical block model was constructed for Mo, W, mfe, Cu, Zn, Pb, and Ag using the ordinary kriging method, and the variational function was developed. (4) Spatial distribution and enrichment characteristics analysis of ore-forming elements are performed to extract geological information, employing the variogram and w(Cu + Pb + Zn + Ag)/w(Mo + W) as predictive indicators. (5) Identifying the western, northwestern, and southwestern areas of the mine with limited mineralization potential, contrasted by the northeastern and southeastern areas favorable for mineral exploration.