SE China is regarded as one of the most important mineral resource bases in China. The spatio‐temporal distribution of the magmatism and mineralization in the area has a distinct pattern due to the uneven intensity of crust–mantle interactions. We analysed gravity, magnetic and magnetotelluric (MT) data from the study area. The lithosphere in the north‐eastern and coastal parts of South China features intense magnetic, low resistivity anomalies and low density of lithospheric mantle material components. Meanwhile, the crust in the Nanling region features high resistivity and low magnetic granitic pluton. As we view from the north‐east to the south‐west, the crust–mantle interaction in SE China weakens unevenly and the magmatic origins for ore‐forming are progressively shallow. In the continental margin area, the subducted plate partially melted and rose along deep faults, interacting with the lithospheric mantle, which created conditions for the formation of the large porphyry Cu deposits. In the inland Nanling region, the Palaeo‐Pacific Plate has subducted to a considerable depth, the influence of deep disturbances was diminished, and therefore the metallogenic magmas of W–Sn deposits are dominated by continental crust remelting granites. While the tectonic environment of the Pb–Zn–Ag polymetallic deposits is in a transitional zone between porphyry Cu deposits and W–Sn deposits, small amounts of femic magma mixed with large amounts of granitic magma to form the mineralized granites. The geophysical data provide corresponding evidence to support the mineralization dynamics model based on oblique Pacific subduction.