Project INDEPTH (InterNational DEep Profiling of Tibet and the Himalaya) is an interdisciplinary program designed to develop a better understanding of deep structures and mechanics of the Tibetan Plateau. As a component of magnetotelluric (MT) work in the 4th phase of the project, MT data were collected along a profile that crosses the eastern segment of the Altyn Tagh fault on the northern margin of the plateau. Time series data processing used robust algorithms to give high quality responses. Dimensionality analysis showed that 2D approach is only valid for the northern section of the profile. Consequently, 2D inversions were only conducted for the northern section, and 3D inversions were conducted on MT data from the whole profile. From the 2D inversion model, the eastern segment of the Altyn Tagh fault only appears as a crustal structure, which suggests accommodation of strike slip motion along the Altyn Tagh fault by thrusting within the Qilian block. A large-scale off-profile conductor within the mid-lower crust of the Qilian block was revealed from the 3D inversion model, which is probably correlated with the North Qaidam thrust belt. Furthermore, the unconnected conductors from the 3D inversion model indicate that deformations in the study area are generally localized.