Determining the spatio-temporal distribution of the deformation tied to the India-Eurasian convergence and the impact of pre-existing weaknesses on the Cenozoic crustal deformation is significant for understanding how the convergence between India and Eurasia contributed to the development of the Tibetan Plateau. The exhumation history of the northeastern Tibetan Plateau was addressed in this research using a new apatite fission track (AFT) study in the North Qaidam thrust belt (NQTB). Three granite samples collected from the Qaidam Shan pluton in the north tied to the Qaidam Shan thrust, with AFT ages clustering in the Eocene to Miocene. The other thirteen samples obtained from the Luliang Shan and Yuka plutons in the south related to the Luliang Shan thrust and they have showed predominantly the Cretaceous AFT ages. Related thermal history modeling based on grain ages and track lengths indicates rapid cooling events during the Eocene-early Oligocene and since late Miocene within the Qaidam Shan, in contrast to those in the Cretaceous and since the Oligocene-Miocene in the Luliang Shan and Yuka region. The results, combined with published the Cretaceous thermochronological ages in the Qaidam Shan region, suggest that the NQTB had undergo rapid exhumation during the accretions along the southern Asian Andean-type margin prior to the India-Eurasian collision. The Cenozoic deformation initially took place in the North Qaidam thrust belt by the Eocene, which is consistent with the recent claim that the deformation of the northeastern Tibetan Plateau initiated in the Eocene as a response to continental collision between India and Eurasia. The immediate deformation responding to the collision is tentatively attributed to the pre-existing weaknesses of the lithosphere, and therefore the deformation of the northeastern Tibetan Plateau should be regarded as a boundary-condition-dependent process.