A controlled-source audio-frequency magnetotelluric (CSAMT) survey has been carried out to investigate potential iron (Fe) and polymetallic (Pb-Zn-Cu) deposits in Longmen region, which is one of the main metallogenic belts in southern China. Conducting geophysical surveys in this area is quite difficult due to mountainous terrain, dense forest, and thick vegetation cover. A total of 560 CSAMT soundings were recorded along twelve surveying lines. Two-dimensional Occam’s inversion scheme was used to interpret these CSAMT data. The resulting electric resistivity models showed that three large-scale highly conductive bodies exist within the surveying area. By integrated interpretation combined with available geologic, geophysical, and geochemical data in this area, three prospective mineral deposits were demarcated. Based on the CSAMT results, a borehole penetrating approximately 250-m depth was drilled at the location of 470 m to the northwest end of line 06, defined with a massive pyrite from the depth of 52–235 m with 7%–16% Fe content, as well as locally high-grade Pb-Zn- and Ag-Ti-bearing ores.