SE Tibet experienced significant deformation during the Late Cenozoic, characterized by clockwise rotation of blocks separated by left-lateral strike-slip faults. Through field surveys, structural analyses and microstructural observations, we identified an early phase of ductile shear zones along three major faults: the Anninghe, Jinhe–Jinghe and Jinpingshan faults. New geochronological and thermochronological data collected from these fault zones and from carbonatites associated with a tear fault between two right-lateral oblique faults provide evidence that this slip occurred before c. 30 Ma. These findings lead to a new conceptual model suggesting that these north–south-trending right-lateral oblique-slip faults, together with the NW-trending left-lateral strike-slip faults in SE Tibet, form a network of large conjugate fractures. The conjugate fracture system, as a result of north- to NE-trending contraction, had a crucial role in controlling the overall tectonic framework of SE Tibet during the Oligocene. By integrating previous research and combining this with our latest findings, we propose a two-phases evolution model of Cenozoic tectonics in the region of SE Tibet, in which a drastic change in kinematics took place from an early phase (before ∼30 Ma) oblique dextral shearing to a late phase sinistral strike-slip faulting since the Miocene.