The northern Alxa orogenic belt, located in the middle segment of the Central Asian Orogenic Belt, is a junction between the North China Craton, Tarim Craton and Mongolian microcontinents. However, its Permo-Carboniferous tectono-palaeogeographic evolution has not been well established. In this study, new zircon U–Pb–Hf isotopic data for the Permo-Carboniferous clastic rocks were used to address the above issue. Based on our dating work and fossil assemblages, we confirmed that the Amushan, Maihanhada, Aqide and Haersuhai formations were formed in the late Carboniferous to early Permian, early to middle Permian, middle Permian and late Permian periods, respectively. The Amushan Formation sandstone in the Zhusileng area contains abundant Palaeozoic zircons (with age peaks at 440 Ma, 475 Ma and 539 Ma) and some Precambrian zircons. These zircon ages and the southeast transgressive direction suggest the provenance to be the local Zhusileng–Hangwula block and the nearby Yagan continental margin. The zircon age pattern with a high proportion of detrital zircons much older than the depositional time and no detrital zircons close to the depositional time suggest an extensional basin depositional setting. The clastic rocks of the Maihanhada, Aqide and Haersuhai formations inherited the source for the Amushan Formation, with a greatly increased input of Permo-Carboniferous volcanic rocks with post-collision or intraplate chemical affinity. Accordingly, a Permo-Carboniferous extensional stage was suggested. Finally, a tectono-palaeogeographic model was reconstructed for the northern Alxa orogenic belt, evolving from a late Carboniferous transgression with crustal extension to early to middle Permian rapid basin filling and a late Permian marine regression.