The Yinkeng orefield is located in the eastern Nanling region, South China. The Nanling region hosts numerous W(-Sn)-dominant, polymetallic deposits related to the widely distributed Mesozoic granites, making it one of the most important W-Sn polymetallic metallogenic belts in the world. In this study, we utilized multiple geophysical methods, including gravity, magnetic, audio-frequency magnetotelluric sounding (AMT), and high-resolution reflection seismic techniques, to detect the underground distribution of granites, strata, and structures. Our aims are to understand better the ore-controlling mechanisms for the large-scale W-Ag-Au-Pb-Zn aggregation, to establish a metallogenic model for this type of mineralization, and to supplement a 3000-m scientific drilling program in the Nanling region for the Chinese SinoProbe Program Project (SP-NLSD-1). In the Yinkeng orefield, an ore-controlling, NE-trending nappe structure is composed of several thrust faults at shallow depths (F1 and F2), which merge into a single major fault at depth. The Pre-Sinian sedimentary rocks of the hanging wall of these faults have much higher velocities, densities and wave impedance than the Carboniferous-Permian sedimentary rocks of the footwall. The slip surface of the nappe, which appears to have low resistivity, extends downward to a two-way travel time of more than 2.5 s, equivalent to a depth of more than 4000 m. Thrusting was from SE to NW, and the fault flattens at depth. The nappe structure may have provided channels for magmas and mineralized hydrothermal fluids. Granites in the Yinkeng area, which are spatially associated with the W-Ag-Pb-Zn orebodies, generally show high resistivity, low polarizability, low seismic velocity and medium magnetism, and their geophysical characteristics have revealed their distribution at depth. Specifically, the Gaoshanjiao granodioritic pluton, closely related to precious metal mineralization, is characterized by low density and high magnetism, allowing us to identify a large buried part of the pluton SE of the exposed body. The Jiangbei granitic pluton, which typically hosts W mineralization, has lower magnetism that reveals a NE-trending extension about 2.2–2.8 km wide at a depth of 16.6 km. One completely concealed granite, the Yinkeng pluton, lies below the nappe structure. It is geophysically similar to the Jiangbei granitic pluton but has an obviously higher magnetic signature. The high magnetism may be due to stratiform polymetallic bodies, which could represent a good exploration target for porphyry-skarn-type, W-Cu-polymetallic deposits (drilling site for SP-NLSD-1). Combined with surface mapping, the geophysical data collected in this study allow us to propose a deep exploration model that can serve as a guide for W-polymetallic ore prospecting in the Nanling and adjacent regions.