The northern Wuyi metallogenic belt contains many polymetallic deposits associated with the Pingxiang–Guangfeng–Jiangshan–Shaoxing Fault (PSF). To study how the PSF has controlled the near-surface mineralization during tectono-magmatic events, a magnetotelluric survey was conducted in the region and a reliable 2D crustal resistivity model was developed. From this model, we inferred that the PSF is characterized by a continuous low-resistivity belt that extends from the surface to the lower crust in the study area and connects to a large conductor in the lower crust. Moreover, the crustal fluid fraction and pressure gradient estimated by our resistivity model exhibited a conspicuous anomaly at the PSF; thus, a material migration model was proposed to explain the source and migration channels of fluids during mineralization. We attributed the Mesozoic minerogenesis to the PSF rework and found that deep fluids were formed in the lower crust and migrated upward through the PSF to the uppermost crust, thereby controlling the large-scale metallogenic belt in the northern Wuyi area. Moreover, we proposed that the formation of mineral system can be divided into three stages, including initially structural formation, structural rework and the migration of ore-bearing fluids.