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The structural relationship between the Qaidam Basin and Qimen Tagh-Eastern Kunlun Range holds important implications for evaluating the formation mechanism of the Tibetan Plateau. Various models have been proposed to reveal the structural relationship, although controversies remain. To address these issues, we analysed the seismic and lithologic data of the Kunbei fault system (i.e. the Kunbei, Arlar and Hongliuquan faults), which lies to the north of the Qimen Tagh-Eastern Kunlun Range within the SW Qaidam Basin. Based on the regional geological framework and our kinematic analyses, we propose that the Cenozoic tectonic evolution of the Kunbei fault system can be divided into two stages. From the Early Eocene to the Middle Miocene, the system was characterized by left-lateral strike-slip faults and weak south-dipping thrust faults based on the flower structure in the seismic section, which is an apparent strike-slip deformation that was identified in the −1510-ms time slice and the root-mean-square amplitude attribute slice. This strike-slip motion was generated by the uplift of the Tibetan Plateau caused by the onset of the Indian-Eurasian collision. Since the Middle Miocene, the Kunbei fault system has undergone intense south-dipping thrusting, and a nearly 2.2-km uplift has been observed in the hanging wall in the Arlar fault. The south-dipping thrusting is the far-field effect of the full collision that occurred between the Indian-Eurasian plates. The lake area in the SW Qaidam Basin has been shrinking since the Middle Miocene and presents widespread delta and fluvial deposits, which are consistent with the proposed tectonic evolution. © 2016, Springer-Verlag Berlin Heidelberg.