By analysis of sedimentary facies correlation of 5 sections of the Jurassic, Combining with seismic data and well data , the Jurassic basin boundary of south margin of Junggar Basin, sedimentary facies evolution and basin pattern are established. The sedimentary facies correlation and paleocurrent measure of Houxia section and Toutun River section suggest that the two sections were formed  in the same sedimentary system during the Early-Middle Jurassic. The sedimentary facies of south margin of Junggar Basin changed from braided river–braided river delta–lacustrine facies to fluvial–lacustrine facies during the Early-Middle Jurassic. During the sedimentary period of Sangonghe Formation of Middle Jurassic, the basin boundary migrated southward to Houxia area and the sedimentary area came to the biggest. Swampy facies was well developed during the sedimentary period of Xisanyao Formation, and the Chepaizi-Mosowan horseback came into being from then on. The Junggar Basin and Tarim Basin were not geographically separated throughout the Early-Middle Jurassic by an ancestral version of the Tianshan Mountains. From the Late Jurassic to the Early Cretaceous, the sedimentary facies was characterized by rapid evolution from braided river–offshore-shallow lacustrine facies to braided river–alluvial fan facies. The distribution of the Kalazha Group conglomerate of Upper Jurassic show that tectonically active background and obvious uplift of the Tianshan Mountains during the Late Jurassic to the early age of Early Cretaceous, led to the widely different sedimentary system of Tarim Basin and south margin of Junggar Basin. The south Junggar Basin shrank northward obviously during the Late Jurassic to the early age of Early Cretaceous and the Bogeda Mountains became another important provenance system of south Junggar Basin.