Based on the field work and interpretation of seismic profiles, the deformation characteristics in the southern margin of the Junggar Basin and their controlling factors are discussed. The deformation in the southern margin of the Junggar Basin is characterized by zonation from the south to the north, segmentation from the west to the east, and layering from the deep to the shallow. The tectonic styles formed are fault-associated folds, including break-thrust folds, fault-propagation folds, detachment folds, fault-bend folds, and fault-arrest folds. The structures were formed mainly in the Quaternary. The third episode of the Himalayan movement affected the trailing edge of the deformation belt, and the movement at the end of the early Pleistocene led the southern margin of the Junggar Basin to deform completely. It has been proved that the coal layer in the Jurassic system played a very important role in the deformation. Its distribution range determined the deformation range, and its thickness determined both the intensity of deformation and the transmission distance of the tectonic stress.