In order to achieve a breakthrough in mineral exploration in the Geluqiduishan mining area of Inner Mongolia, comprehensive geophysical methods such as magnetic method, audio magnetotelluric method, high-density electrical method, and portable X-ray fluorescence method were used to prospect. The coexisting magnetic anomalies indicate interlayer slip fault structures, while high magnetic anomalies reflect the distribution of granite intrusive rocks, and mineralized zones (bodies) are distributed as a whole on the southeast side of slip fault structures, showing weak or no magnetism. The high resistance anomaly zones in the joint electrical resistivity sections reveal that the granitic intrusive rocks extend along a NE-trending direction, with a trend of widening from southwest to northeast. The resistivity gradation zones reflect secondary fault structures. Geochemical anomalies and comprehensive analysis suggest that deep intrusive rocks are closely related to mineralization, with fault structures and secondary fault structures developed along the contact zones between the intrusive bodies and surrounding rocks. Mineralization (bodies) or veins around the rock mass migrate and store along the fault structures, with some exposed on the surface. The integrated geochemical and geophysical exploration provided critical fault structures, intrusive body distribution, and enrichment zones of mineralizing elements closely related to prospecting in this concealed polymetallic mining area, offering important guidance for mineralization law research and prospecting directions.