The Lower to Middle Permian terrestrial successions in the southern Junggar and Turpan basins provide a wealth of information regarding the paleoclimatic and paleogeographic evolution of mid-latitude NE Pangea. Two sections, namely the Xiaolongkou section in the southern Junggar Basin and the southwest (SW) Tarlong section in the Turpan Basin, were systematically studied using detrital zircon geochronology and whole-rock geochemical analysis. Stratigraphic studies suggest that, in both sections, the Lucaogou and Hongyanchi formations are dominated by lacustrine deposits, while the Quanzijie Formation represents mixed fluvial-lacustrine and loess environments. The Lucaogou Formation displays low CIA (Chemical Index of Alteration) values and Th/U ratios, suggesting semiarid to arid conditions in both sections. The Hongyanchi Formation shows low to intermittently moderate CIA values and Th/U ratios, indicating variably semiarid-arid conditions alternating with subhumid-semiarid episodes. The lower part of the Quanzijie Formation reflects subhumid-semiarid to semiarid-arid conditions, while the upper part of the Quanzijie Formation mainly records semiarid-arid and shifts into subhumid conditions toward the top. Detrital zircon and element data indicate that, within each section, all three formations display similar zircon age distributions and geochemical characteristics, suggesting no significant changes in provenance during deposition. However, the provenance characteristics of the two sections differ from each other; the Xiaolongkou section is rich in felsic material, with two detrital zircon age peaks, while the SW Tarlong section contains more mafic components, with a single peak in detrital zircon age spectrum. This suggests that the greater Junggar-Turpan Basin was highly partitioned with several independent provenance systems active during the Early-Middle Permian. The abrupt change in depositional environments in both sections may have resulted from uplift of the North Tian Shan, which induced rapid regression of the lakeshore and uplift of sediment source and catchment areas.