The Xining Basin is located in the northeastern Qinghai–Tibetan Plateau, and its continuous Cenozoic strata record the entire uplift and outgrowth history of the Tibetan Plateau during the Cenozoic. The newly obtained apatite fission track data presented here shows that the Xining Basin and two marginal mountain ranges have experienced multiphase rapid cooling since the Jurassic, as follows. In the Middle–Late Jurassic, the rapid exhumation of the former Xining Basin resulted from collision between the Qiangtang Block and the Tarim Block. During the Early–Late Cretaceous, the former Xining Basin underwent a tectonic event due to marginal compression, causing the angular unconformity between the Upper and Lower Cretaceous. In the Late Cretaceous to the Early Cenozoic, collision between the Qiangtang Block and the Lhasa Block may have resulted in the rapid exhumation of the Xining Basin and the Lajishan to the south. In the Early Cenozoic (ca. 50–30 Ma), collision between the Indian and Eurasia plates affected the region that corresponds to the present northeastern Qinghai–Tibetan Plateau. During this period, the central Qilian Block rotated clockwise by approximately 24° to form a wedge-shaped basin (i.e., the Xining Basin) opening to the west. During ca. 17–8 Ma, the entire northeastern Qinghai–Tibetan Plateau underwent dramatic deformation, and the Lajishan uplifted rapidly owing to the northward compression of the Guide Basin from the south. A marked change in subsidence occurred in the Xining Basin during this period, when the basin was tectonically inverted.