Magma emplacement can restrict the nature and distribution of an ore deposit, and is an important topic for the study of mineralization mechanisms. Previous studies of magma emplacement have focused mainly on the superimposed mineralization of multi-stage magma in time, whereas the superimposed characteristics and mineralization of different magma emplacement in space are unclear. We estimate a 3-D multiple geophysical model in the Shuangjianzishan Ag–Pb–Zn district, northeastern China, using gravity, magnetic, magnetotelluric and seismic data. The model describes the distribution of buried magmatic rocks related to mineralization in the ore district and highlights the detailed structure and connection of volcanism and intrusion. The volcanism is characterized by a tree-like structure consisting of a near-conical channel and an annular fault system; the intrusion appears as a dome-shaped structure, and its lateral distribution is controlled by faults. The geophysical results reveal a deep fault system connecting volcanism and intrusion. Combining the results with regional geology, petrophysical properties and borehole information, we propose a composite metallogenic model for the ore district, which is that the volcanism caused the ore-bearing magma to migrate to the present-day location of the base of the ore deposit through the deep fault system, and formed an intrusive complex with the ore-bearing magma emplaced in a dome below the present-day location of the deposit. This resulted in the formation of complex and fault-controlled ore bodies. Reviewing the global metallogenic characteristics related to magmatism, our results demonstrate the magma emplacement pattern of a composite volcanic-intrusive system may be an important factor for the formation of super-large deposits.