Anisotropy of magnetic susceptibility (AMS) analyses and structural observations of Triassic flysch in the Tsetang area, SE Tibet, were carried out to assess the Cenozoic tectonic evolution and kinematics of deformation of the eastern Tethyan Himalaya Thrust Belt. We analysed a total of 202 standard-sized specimens from four sample sites across the Renbu–Tsetang Thrust from north to south. Rock magnetism and the detailed mineralogy demonstrated that ferromagnetic and paramagnetic minerals both contribute to the AMS. However, the paramagnetic contribution is dominant in the study area. The AMS results, together with field-based structural investigations and analyses of microstructures, revealed that layer-parallel shortening (LPS) was accommodated mainly by isoclinal folds, cleavage, and thrust faults. Shear fabrics (K1 axes oriented parallel to the direction of local tectonic transport) were found mainly in the north thrust fault zone and were linked to fault movement. Microstructural analyses of quartz and metamorphic minerals such as muscovite (sericite) and chlorite in slates and sandstones imply that the peak temperature during the deformation did not exceed 300 °C. The shear AMS fabric in north Qonggyai, near the thrust zone, shows that the strain variation is related to the main activity (11–19 Ma) of the Renbu–Tsetang Thrust. The magnetic lineation that plunges towards the east in the southern Qonggyai area indicates extension that was linked to an E–W extensional event during the early Miocene. Based on the available geochronological data, two stages of tectonic deformation can be defined: (a) syncollisional layer-parallel shortening at ~40 Ma ago, and (b) E–W extension and continuing compaction resulting in shearing at 11–19 Ma.