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Uplift of the Tibetan Plateau and the distribution of deformation across it are the result of India-Asia collision, which bring an opportunity of understanding intracontinental tectonics in the context of continent-continent collision. The Tibetan Plateau is bound on the northern margin by the Qilian Shan thrust belt and the strike-slip Haiyuan fault. These Cenozoic fault systems play a critical role in accommodating continental convergence, yet the initiation age, deformation sequence and mechanisms of deformation are debated. In this study, integrated geologic mapping, field observations, and apatite fission track thermochronology were conducted to constrain the initiation ages of the localized thrust faults and the exhumation history of the central and northern Qilian Shan, northern Tibet. Our analyses reveal the central and northern Qilian Shan underwent rapid cooling during the Cretaceous as a result of a far-field tectonic event. In the Eocene-Oligocene, a period of thrust-related cooling occurred along the Shule Nan Shan, Tuolai Nan Shan and Tuolai Shan faults. Reactivation of the proximal thrust faults and initiation of the western segment of the Haiyuan fault occurred at ca. 16 Ma and drove final accelerated Miocene cooling and denudation to the surface. We argue that the Qilian Shan thrust belt has persisted as the stationary and internally deformed northern boundary of the Himalayan-Tibetan orogen since the early Cenozoic, involved overprinting out-of-sequence development starting by Eocene related to initiation of India-Asia collision, and the basins and ranges across the northern Tibetan Plateau have since experienced multi-phase of growth. • The central and northern Qilian Shan experienced three-pulse cooling starting in the early Cretaceous. • Thrust systems and Haiyuan fault across the Qilian Shan initiated in Eocene-Oligocene, and Miocene, respectively. • The Qilian Shan thrust belt underwent out-of-sequence deformation starting in Eocene shortly after the Indo-Asia collision. [ABSTRACT FROM AUTHOR]