Overpressure can be widely observed in the Jurassic, Cretaceous and Paleogene reservoirs in the southern margin of the Junggar Basin, northwest China. The study region was subjected to intense tectonic stress from the neighbouring North Tianshan Mountains since the Miocene. However, the causes of tectonic stress-induced overpressure are still poorly understood. In this study, we considered the plots of sonic velocity against density and vertical effective stress and applied numerical simulations and geological analysis to determine the origin of overpressure with respect to mudstone and sandstone in the area under study by investigating the compaction of mudstone and analysing the overpressure distribution. Our results indicate that the most overpressured mudstone in the second and third structural belts and the east of the Sikeshu Sag exhibits abnormally high porosity, which is obvious from the regional seal mudstone of the Paleogene Anjihaihe and Lower Cretaceous formations. The overpressure in these mudstones can be mainly attributed to the increase in vertical stress and horizontal tectonic stress (HTS). The current overpressures in the reservoir sandstone of the second and third structural belts as well as towards the east of the Sikeshu Sag are mainly induced by HTS, overpressure transfer and increase in vertical stress. The contribution of the overpressure associated with the generation of HTS to the total overpressure differs in different belts. This contribution ranges from 28.5% to 69.2%, 21.2% to 46.2% and 16.3% to 34.8% in the second, the third structural belt and the east of the Sikeshu Sag, respectively. Thus, HTS can be the primary contributor to the reservoir overpressure in many zones in the area under study.