On 1 June 2022, a magnitude 6.1 earthquake struck the southern segment of the Longmenshan fault zone on the eastern edge of the Tibetan Plateau, once again causing casualties and economic losses. Understanding the deep-seated dynamic mechanisms that lead to seismic events in the Lushan earthquake area and assessing the potential hazards in seismic gap areas are of significant importance. In this study, we utilized 118 magnetotelluric datasets collected from the Lushan earthquake area and employed three-dimensional electromagnetic inversion with topographic considerations to characterize the deep-seated three-dimensional resistivity structure of the Lushan earthquake area. The results reveal that the Shuangshi–Dachuan fault in the Lushan earthquake area can be divided into two relatively low-resistivity zones: a western zone dipping southeastward and an eastern zone with a steeper slightly northwestern dip. These two zones intersect at a depth of approximately 20 km, forming an extensional pattern resembling a “Y” shape. The epicenters of both the 2013 and 2022 Lushan earthquakes are primarily located in the upper constricted portion of the pocket-like low-resistivity body at depth. The distribution of seismic aftershocks is confined within the region enclosed by the high-resistivity body, following the pattern of the Y-shaped low-resistivity zone.