The Qaidam Basin is the one of the three major petroliferous basins in northeastern Tibetan Plateau, which has experienced multiphase superimposition and transformation. The study of thermal history not only plays an important role on revealing the tectonic origin of the Qaidam Basin and the forming mechanism and uplift history of the Tibetan Plateau, but also can provide scientific evidence for the assessment of oil and gas resources. This work used?balanced cross-section technique and apatite fission track ages with modeling of fission track length distribution to infer that the eastern Qaidam Basin has experienced significant tectonic movement in the Early Jurassic movement (~200 Ma), which caused the carboniferous uplift and denudation, the geological movement in the Late Cretaceous, characterized by early stretching and late northeast-southwest extrusion; the Himalayan movement in multi-stage development in eastern Qaidam Basin, which can be divided into the early Himalayan movement (41.1–33.6 Ma) and the late Himalayan movement (9.6–7.1 Ma, 2.9–1.8 Ma), and large-scale orogeny caused pre-existing faults reactivated in late Himalayan movement. On the basis of burial history reconstruction, the thermal history of eastern Qaidam Basin was restored. The result shows that the thermal history in eastern Qaidam Basin shows slow cooling characteristics; the paleo-geothermal gradient of eastern Qaidam Basin was 38–41.5℃/km, with an average value of 39.0℃/km in the Late Paleozoic, 29–35.2℃/km, with an average value of 33.0℃/km in the Early Paleogene; the geothermal gradient of the Qaidam Basin increased in the Late Paleogene, which was similar to the present geothermal gradient in the Late Neogene. The characteristics of the tectono-thermal evolution since Paleozoic in the eastern Qaidam Basin are mainly controlled by magmatic thermal events in the study area.