The thermal evolution of the Junggar Basin, northwest China, was evaluated based on the thermal modelling results of 59 wells by using vitrinite reflectance (Ro) and apatite fission track (AFT) data. The thermal history indicates a cooling process of the basin since the Permian, but some differences in thermal evolution existed among the six structural units of the basin due to tectonic movements. The Junggar Basin was a ‘hot basin’ during the Permian, after which a cooling process with normal heat flow values occurred during the Mesozoic. Then the basin became a ‘cool basin’ from the beginning of the Tertiary. The average heat flow of the whole basin was 80 mW m−2 at the beginning of the Permian, then it decreased to 68 mW m−2 at the end of the Permian, to 63 mW m−2 at the end of the Triassic, 55 mW m−2 at the end of the Jurassic, 50 mW m−2 at the end of the Cretaceous and 42 mW m−2 at the present day.
The heat flow distribution of the basin at different geological times also shows the thermal evolution characteristics of the Junggar Basin. At the beginning of the Permian, the highest heat flow, 85 mW m−2, occurred in the central basin and the eastern part of the basin, but the lowest heat flow was distributed along the southern and western basin margins, down to 70 mW m−2. The heat flow values were between 45 mW m−2 and 65 mW m−2 at the end of the Jurassic, with the lower value of 45 mW m−2 at the southern basin margin. The highest heat flow value again occurred at the southern end of the Luliang Uplift, at the northern part of the Central Depression and at the Eastern Uplift area during that period. At the end of the Cretaceous, it was down to 40–55 mW m−2. The lowest heat flow occurred at the Southern Margin and in the Wulungu Depression, and the highest value in the Eastern Uplift area.
The tectonic subsidence also supports this thermal evolution of the basin. The rapid decrease of heat flow during the Tertiary in the Southern Margin of the basin may be caused by the uplift of the Tianshan Mountain. These heat flow data can provide useful parameters for the study of the Junggar Basin. Palaeoheat flow data are the critical parameter for hydrocarbon generation calculations. The results of this study provide a foundation for hydrocarbon generation history modelling and petroleum resource assessment in the Junggar Basin, which are important factors in the exploration of the Wulungu Depression and the study of stratigraphic and subtle traps in the Central Depression.