Magnetotelluric (MT) geophysical profiling has been applied to the determination of the deep structure of the Longling–Ruili fault (LRF), part of a convergent strike-slip fault system, underneath thick Caenozoic cover in Ruili basin in southwestern Yunnan, China. The recorded MT data have been inverted using a two-dimensional (2-D) nonlinear conjugate gradients scheme with a variety of smooth starting models, and the resulting models show common subsurface conductivity structures that are deemed geological significant. The models show the presence of a conductive (5–60 Ω m) cover sequence that is thickest (1–1.5 km) in the centre of the basin and rapidly pinches out towards the margins. A half-graben structure is interpreted for the Ruili basin. This is underlain by about 7–10 km thick upper crustal layer of high resistivity (>200–4000 Ω m) that is dissected by steep faults, which we interpret to flatten at depth and root into an underlying mid-crustal conductive layer at about 10 km depth. The mid-crustal layer does not appear to have been severely affected by faulting; we interpret it as a zone of partial melt or intracrustal detachment. The MT models suggest SE directed thrusting of basement rocks in the area. The Longling–Ruili fault is interpreted as a NW-dipping feature bounding one of the identified upper crustal fragments underneath Ruili city. We suggest that MT imaging is a potent tool for deep subsurface mapping in this terrain.