Shallow-water lacustrine delta sandstone in large continental sag basins have become the most important target for the stratigraphic reservoirs. The Junggar Basin was a continental sag basin in the Mesozoic. From the Early to Middle Jurassic, the Tian Shan experienced a regional peneplanation, providing a very favorable topographic condition for the developing of shallow-water deltas. However, studies on the sedimentary facies of the Lower to Middle Jurassic generally lack of systematicness and remain controversial. This article selected several sections in the southern Junggar Basin and carried out detailed sedimentary characteristic analysis and sedimentary facies identification in each section. Three shallow-water lacustrine deltas were identified in the southern Junggar Basin: 1) shallow-water braid plain delta, well developed in the Badaowan Formation and characterized by threadiness near-sources, abundant coarse-grained sediments, widespread distributary channels and undeveloped mouth bars; 2) shallow-water mouth-bar meandering-river delta, common in the Sangonghe Formation and showing well-developed mouth bars generally reformed by lake waves; 3) extremely shallow-water meandering-river delta, well developed in the Xishanyao Formation and characterized by widespread delta plain and undeveloped delta front. According to the lake delta evolution, a lake transgression to regression process happened in the southern Junggar Basin from the Early to Middle Jurassic, which is inconsistent with the continuous retrogradation of provenance and expansion of the Junggar Basin, indicating a relatively dry climate or basement uplift of the Junggar Basin during deposition of the Xishanyao Formation in contrast to the Early Jurassic Badaowan and Sangonghe Formations. Climate changes and basin basement slowly uplift collectively controlled the evolution of accommodation.