Field and microscopic structural investigations, trace element and C–O isotopic analyses of calcite, zircon U-Pb dating of dikes, and wide-field electromagnetic sounding are conjointly conducted in the middle part of the Qin-Hang metallogenic belt to decipher the spatial-temporal evolution and genetic relationship of structure-magma- mineralization. The data reveal four deformation events: D1 is a W-to-E-thrusting event; D2 is characterized by SE-to-NW thrusting; D3 is a NW-SE-oriented extensional event accompanied by large-scale magma intrusion and W–Sn and Cu–Pb–Zn mineralization; D4 is a dextral strike-slip event after mineralization. Two stages of calcite are identified during D₃ and Stage II calcite is characterized by LREE-enriched REE patterns, with low δ¹⁸OSMOW (from 9.78‰ to 12.3‰), identical to those of calcite in the deposits, confirming that they are closely related to mineralization. Wide-field electromagnetic profiles further display the geometric characteristics of structures, granitic plutons, and orebodies from shallow to deep (~5 km) level. It is believed that some giant concealed W-Sn and Cu-Pb-Zn orebodies are developed in the contact zones between plutons and limestone at a depth of 1.5-4 km. It is reasonable to suggest that this method is feasible for the study on the deep exploration of W-Sn and Cu-Pb-Zn polymetallic deposits.