Geophysical exploration techniques are crucial in facilitating accurate mineral prospecting predictions, but relying solely on single methods can introduce uncertainties. In this study, we employed audio-frequency magnetotelluric (AMT) methods, complemented by gravimetric surveying and high-resolution magnetic profiling in the Yongxin gold deposit. Utilizing advanced three-dimensional modeling techniques, we were able to precisely delineate the lithological variations and deep-seated mineralization features inherent to the area. The inversion and interpretation of cross-sectional AMT data illuminated the subsurface structure down to a depth of 1.5 kilometers. This enhanced data reliability was achieved through an integrated interpretation constrained by gravity, magnetic, and electrical datasets, thereby enabling a more accurate inference of the deeper geological framework. Furthermore, by amalgamating regional geological data, drilling information, and additional datasets, we uncovered the characteristics of deep mineralization, the three-dimensional configuration of mineralization-related rock masses, and the spatial orientation of known ore deposits. This approach facilitated a transparent visualization of the deeper geological formations. A thorough analysis was conducted on the distribution patterns of ore-controlling structures and exploration markers. Consequently, we have established a geological-geophysical model tailored for mineral exploration within the study area, which provides an effective reference for future deep exploration work.