We performed a study on using an integrated geologic model in mineral exploration at depth. Shizishan ore field, in the western part of the Tongling ore district, Anhui Province in China, is well known for its polymetallic deposits and recent deep discovery of Dongguashan deposit at around 1000-m depth. Understanding the 3D structure and delineating the locations and variations of the intrusions and ore-controlling strata in the study area are essential for selecting deep mineral targets. A pilot 3D geologic model, covering an area of 11 × 16 km and extends to a depth of 3 km, has been constructed by interactive gravity and magnetic inversions to define the geometry, depth, and physical properties of geologic bodies at depths. The 3D visualization of the results assists in understanding the spatial relations between various intrusive units and the ore-bearing strata. The model has confirmed most previous knowledge, but also revealed new features of different folds and intrusions that are important for planning future exploration at large depths. Several deep targets have also been predicted by combining the conceptual mineralization model in the district with the 3D geologic model. Our study demonstrates the potential of using gravity and magnetic data with geologic constraints to build 3D models in structurally complex areas for the purpose of mineral exploration at depth and under cover.