A comparsion of regional stratigraphy, typical measured sections, lithofacies and depositional environments suggests that the western and eastern part of the southern Junggar Basin (roughly along 88°E) have distinctively different rock assemblages, stratigraphic sequences, sedimentary characteristics, and depositional environments. The western part of the southern Junggar Basin is characterized by the clastic-volcanic-volcaniclastic rock assemblages, while the eastern part is composed mainly of carbonate-volcanic-volcaniclastic rock assemblages. In the western part of the southern Junggar Basin, the Cisuralian-Guadalupian strata are generally absent or deeply buried. The Lopingian-Early Triassic strata are dominated by conglomerates with some sandstones and minor mudstones, revealing features of an alluvial fan system. The Middle-Late Triassic strata are composed principally of fine-grained clastic rocks which are interpreted as belonging to a lacustrine system. The depositional environment in the eastern part of the southern Junggar Basin is interpreted as a deep-water turbidite in the Pennsylvanian, followed by a shallow marine environment in the Cisuralian-Guadalupian. In the Guadalupian Lucaogou Formation, the oil shale and carbonate rock are broadly exposed in the Bogda Mountains, suggesting occurrence of a rifting-drifting tectonic cycle in this period. Subsequently, the whole Junggar Basin is characterized by the fluvial and lacustrine systems from the Lopingian, which consist mainly of fine to corase-grained clastic rocks. In the Middle-Late Triassic, the drainage system had expanded with a levelled process, and the eastern part of the southern Junggar Basin is composed mainly of deltaic and shallow lacustrine clastic rocks. This study shows that the Permian-Triassic sediments in the southern Junggar Basin and the adjacent regions are dominated by rifted and depressional sedimentation, but there are differences between the western and eastern part of the southern Junggar Basin in their rift level.