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[Display omitted] • Cenozoic double-layered structure was identified in the western Qaidam Basin. • The Qaidam Basin suffered much stronger shortening deformation in west than east. • The double-layered structure in the western Qaidam Basin was initiated at Pliocene. • Double-layered structure was due to far-field effect of the India-Asia collision. The Qaidam Basin in the northern Tibetan Plateau lies above over 3000 m elevation above sea level, being the inland terrestrial basin with the highest altitude in the world. This basin is surrounded by the Eastern Kunlun, Altyn and Qilian Mountains, and represents a key area to decipher the tectonic and kinematic evolution of the northern Tibetan Plateau during Cenozoic times. The Cenozoic deformation of the Qaidam Basin is synchronous with the uplift of the northern Tibetan Plateau. The structural coupling between Cenozoic shallow and deep deformation systems in the Qaidam Basin is complicated and poorly understood, because of the lack of studies of the deformation at the depth. Based on the detailed structural analysis of the Honggouzi and Nanyishan anticlines in the western Qaidam Basin, we found that the fault-propagation fold was usually developed in the shallow part and "Y" shaped thrust faults occur at both sides of the anticlinal core, while fault-bend folds developed above the bottom detachment fault in the deep, which together constitute the Cenozoic double-layered structure (DLS). The DLS is relatively well developed in the northwest and gradually disappears to the southeast in the Qaidam Basin, indicating that the deformation and shortening in the western Qaidam Basin is much stronger than that in the eastern Qaidam Basin. The initial formation time of the DLS started from Pliocene (Shizigou Fm.) and continue to present, which supports that the Qaidam Basin was a "plate-shape-like" compressive flexing basin without obvious deformation during Eocene to Pliocene. The formation of the DLS in the western Qaidam Basin was due to the continuing N/NNE-directed compression in the southwest and the large-scale sinistral strike-slip displacement along the Altyn Tagh fault in the northwest related to the far-field stress effect of the India-Asia collision. [ABSTRACT FROM AUTHOR]