Based on the results of 216 points of magnetotelluric sounding carried out in the Qinling and its adjacent region, we established a 3 D electrical structure model of the crust and upper mantle. The axes of electric resistivity anomalies are mainly east west trending at the depths of 30 km and 90 km, and nearly north south at the depth of 150 km. The low resistivity layers in the upper mantle (LRLIUM) of the North China massif are shallow and about 60 80 km deep. The Yangtze massif was a downwarping region of LRLIUM, which is generally deeper than 120 km. As a whole, the Qinling orogen is situated above the depth transition zone of LRLIUM. Within the zone there are some local uplifts and depressions. In the study area, there are a series of uplift zones of LRLIUM, which may be the passages of the upwelling mantle material. Endogenetic ore deposits since the Mesozoic are mostly distributed above the salient of LRLIUM or above its two sides where the gradient is steep. Molybdenum and wolfram deposits are distributed above the ridge of the salient of LRLIUM, and copper, lead, zinc and gold deposits are distributed above the gradient zones beside the salient of LRLIUM. Deposits are fewer above the depression of LRLIUM. So, the relationship between deposit distribution and LRLIUM’s shape can provide information for prognostication of endogenetic ore deposits. Based on the results of 216 points of magnetotelluric sounding carried in the Qinling and its adjacent regions, we established a 3 D electrical structure model of the crust and upper mantle. The axes of electric resistivity anomalies are mainly east west trending at the depths of The low resistivity layers in the upper mantle (LRLIUM) of the North China massif are shallow and about 60 80 km deep. The Yangtze massif was a downwarping region of 30 km and 90 km LRLIUM, which is generally deeper than 120 km. As a whole, the Qinling orogen is situated above the depth transition zone of LRLIUM. Within the zone there are some local uplifts and depressions. In the study area, there are a series of uplift zones of LRLIUM, which may be the passages of the upwelling mantle material. Endogenetic ore deposits since the Mesozoic are mostly distributed above the salient of LRLIUM or above its two sides where the gradient is steep. Molybdenum and wolfram deposits are distributed above the ridge of the salient of LRLIUM, and copper, lead, zinc and gold deposits are distributed above the gradient zones beside the salient of LRLIUM. So, the relationship between deposit distribution and LRLIUM’s shape can provide information for prognostication of endogenetic ore deposits.