In the Qaidam Basin, on the Northeastern Qinghai–Tibet Plateau, the thermal evolution of western and northern sub-basins was analysed using apatite fission track (AFT) data and vitrinite reflectance data from 27 wells. This study shows that thermal gradients decreased during the evolution of the basin, but there existed some differences in thermal evolution between the west and north of the basin, due to different tectonic movements. The thermal gradients in Paleocene–Miocene in the west and in Jurassic times in the north were more than 30°C km−1, exceeding present-day gradients. These thermal data can provide useful parameters for the study of the Qaidam Basin and Qinghai–Tibet Plateau. Palaeotemperature data are the critical parameter for hydrocarbon generation calculations. The results in this study provide a foundation for hydrocarbon generation history modelling and petroleum resources assessment in the Qaidam Basin.