Abstract The Beishan orogen, a significant component of the southern Altaids, presents an opportunity for investigating the intracontinental deformation and exhumation history of the Altaids during the Mesozoic era. Although previous studies indicated that the Beishan orogen has experienced multiple reactivation since the late Mesozoic, the precise extent of these events remains poorly constrained. Here, we provide a comprehensive synthesis of field observations and apatite fission track (AFT) thermochronological dating throughout the Beishan orogen. Detailed field observations confirmed four major E-W trending thrusts in our study area. Based on the youngest truncated strata associated with the thrusts and previous dating results from neighboring regions, we propose that these thrust sheets likely developed in the late Middle Jurassic. AFT dating results from seven pre-Mesozoic granitoid samples and associated with thermal history modeling demonstrate that the Beishan orogen experienced a rapid basement cooling during the mid-Cretaceous (~115–80 Ma). Moreover, a compilation of previously published and newly gained AFT data reveals a comparable mid-Cretaceous cooling event in other parts of Central Asia, such as Qilian Shan, Eastern Tianshan, and Altai-Sayan. This observation suggests that the mid-Cretaceous cooling event is more likely to be regional rather than localized. This mid-Cretaceous cooling pulse is interpreted as a tectonic exhumation controlled by boundary faults and related to the rotation of the Junggar and Tarim basins. These processes are linked to distant plate-margin events along the Eurasian continent.