The Chinese Altai, as an accretionary orogen developing from the Cambrian to Carboniferous, was modified by Permian deformation, metamorphism and magmatism in response to the collision with the East Junggar. The tectonic processes of the collision and the timing of related deformation and metamorphism are still enigmatic. Here we present new 40Ar/39Ar dating results for granitic gneisses and amphibolites exposed in the Qiongkuer Domain in two areas (Alahake and Fuyun) of the southern Chinese Altai. The amphiboles from both Aalaheke and Fuyun areas yield consistent 40Ar/39Ar plateau ages at 265.9±1.7Ma and 270.1±3.1Ma. In contrast, the biotites from two areas show distinct 40Ar/39Ar ages of 232.0±2.1Ma and 226.8±1.7Ma for the Alahake area, and 245.1±1.5Ma and 264.5±2.2Ma for the Fuyun area, respectively. Given that 40Ar/39Ar ages are younger than the Permian high temperature metamorphism at ∼299–277Ma as constrained by metamorphic zircons in the Qiongkuer Domain, we interpret these 40Ar/39Ar ages to record the cooling history of two areas. Compatible amphibole ages in both areas indicate a similar exhumation age along the Qiongkuer Domain cooling through 550°C at ∼270–265Ma, which may have been associated with the development of the sinistral Erqis Shear Zone during the collision between the Chinese Altai and the East Junggar. The subsequent exhumation processes were variable in different areas of the Qiongkuer Domain as showed by the distinct biotite ages, which may indicate along-strike variation of cooling processes from 550°C to 300°C in the Qiongkuer Domain.