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The Tibetan Plateau (TP) is the highest plateau in the world, which has been the focus of Cenozoic geological studies. The Northeast Tibetan Plateau (NETP) is a key location to decipher the Cenozoic evolution history of the TP. Understanding the building of the Qimen Tagh Mountains located in NETP will help to constrain the development of the northern boundary of the main TP, test the existence of a Paleo-Qaidam Basin and test the eastward growth model of the TP. In this study, granite samples from the Qimen Tagh Mountains were dated by LA-ICPMS and apatite fission track (AFT). The LA-ICPMS zircon U–Pb ages give two magmatic events around ~ 405 and ~ 255 Ma from two different sites. AFT modeling shows that the initial uplift took place at ~ 40–30 Ma in these mountains, which should be controlled by the Altyn Tagh Fault. Compiling previously low-temperature thermochronometry results, it reveals that the initial Cenozoic uplift of the northern boundary of the TP (Qimen Tagh and East Kunlun mountains), soon after the India–Eurasia collision in the southern TP, has divided the Paleo-Qaidam Basin into several sub-basins. The approximate NE–E growth process occurred along the lithospheric Altyn Tagh and Kunlun faults. The current basin and range morphology of the NETP took place around ~ 8 Ma. [ABSTRACT FROM AUTHOR]