To better understand the geothermal system of the Gonghe Basin, we deployed 471 magnetotelluric survey points with an average distance of 2~3 km, covering the eastern and southern areas of the Basin. We used ModEM inversion software to carry out 3D inversion of 431 survey points and established a 3D-electrical model at a depth of 50 km in the area. The resistivity model shows that the low resistivity in the shallow part of the basin is related to the Cenozoic loose sedimentary cover, while the resistivity values of the mountains around the basin and the magmatic rock uplift zone are higher. The electrical model also shows that the high-conductivity layer is widely distributed in the middle and lower crust (15~35 km) of the basin, and direction of the high-conductivity layer is consistent with that of NW–SE fault in the basin. These high-conductivity layers may be the principal reason for the high heat flow values in the Gonghe Basin. Our resistivity model also shows that there is an obvious discontinuity between high- and low-resistivity blocks at different depths in the middle and upper crust. These discontinuities are consistent with the faults observed on the surface, which are related to the strong topographic relief. Our electrical model shows that these faults in the middle and upper crust are connected with the high-conductivity layer as the channel of heat transfer to the shallow part. Finally, the heat energy is enriched in the Triassic granite to form dry hot rock (HDR). The 3D-magnetotelluric imaging results depict the 3D-distribution characteristics of the geothermal system in the eastern and southern parts of the Gonghe Basin.