The present topography of the northern Tibetan Plateau is characterized by the northwest-trending Eastern Kunlun Range, Qaidam Basin, and Qilian Shan, which figure importantly into the evolution and mechanism of Tibetan plateau development during Cenozoic Indo-Asian convergence. Understanding the Cenozoic deformation history and the source-to-sink relationship through time has significant implications for deciphering the growth history of the northern Tibetan Plateau. Despite decades of study, the timing, pattern, and mechanisms of deformation across the northern Tibetan Plateau are still vigorously debated. The North Qaidam thrust belt, located between the Qaidam Basin and Qilian Shan thrust belt, provides a valuable record of Cenozoic deformation in the northern Tibetan Plateau. Here, we present the results of new geologic mapping, structural and sedimentology analysis, and apatite fission track thermochronology to constrain the Cenozoic evolution history and reconstruct the paleogeomorphology of the eastern domain of the North Qaidam thrust belt and its foreland, the Wulan Basin. Our analyses reveal the North Qaidam thrust belt experienced multi-phase exhumation since the Cretaceous. A period of Eocene localized thrust-related uplift of the North Qaidam thrust belt initiated shortly after India-Asia collision, and lower erosion rates in the Oligocene allowed the thrust belt to expand along-strike eastward. Local uplift shed sediments to the southwest, directly into the Qaidam Basin. Reactivation of the proximal thrust faults and initiation of the northwest-striking right-slip Elashan fault at ca. 15–10 Ma drove the final accelerated mid-Miocene cooling and denudation to the surface. This phase of deformation established the overall framework morphology of the northeastern margin of the Tibetan Plateau, including the overall structure of the basins and ranges.