New evidence worldwide has linked the surface locations of mineral deposits and their crustal-scale electrical conductivity footprint. We examine the relationship between the Gangdese Miocene porphyry copper deposits, Tibetan Plateau, and the electrical conductivity signature from a three-dimensional model generated from 311 magnetotelluric measurements. The distribution of electrical resistivity throughout the crust and the conductance within the mid-lower crust (depth range of 25–70 km) is analyzed. The results clearly show that the large and ultra-large Miocene porphyry copper deposits coincide spatially with conductive zones and areas of very-high conductance (>10,000S) in the mid-lower crust. Computations are undertaken to determine the influence of water-bearing silicate melts and alkali-bearing (Na+ and K+) fluids on conductivity. Based on this, the bulk conductivity is interpretated to be caused by a system of alkali-rich volatile-rich partial melt. The alkali-rich volatile-rich magmatic-hydrothermal fluids facilitate the migration and concentration of metal ions originating in deep areas. The volumes necessary are much less than partial melt alone and can thus help to reconcile large conductivity variations with small seismic velocity variations. The electrical structure indicates the magma source area of anatexis in the lower crust, a multi-stage magmatic system with large mid-crustal and small upper-crustal magma reservoirs, and complex pathways related to rift zones. We determine that the conductive zones in the mid-lower crust have an influence on the development of the mineralization and the location of the mineral belt.