According to the differences of structural deformation characteristics, the southern margin of the Junggar basin can be divided into two segments from east to west. Arcuate thrust-and-fold belts that protrude to the north are developed in the eastern segment. There are three rows of en echelon thrust-and-fold belts in the western segment. Thrust and fold structures of basement-involved styles are developed in the first row, and décollement fold structures are formed from the second row to the third row. In order to study the factors controlling the deformation of structures, sand-box experiments have been devised to simulate the evolution of plane and profile deformation. The planar simulation results indicate that the orthogonal compression coming from Bogeda Mountain and the oblique compression with an angle of 75° between the stress and the boundary originating from North Tianshan were responsible for the deformation differences between the eastern part and the western part. The Miquan-ürümqi fault in the basement is the pre-existing condition for generating fragments from east to west. The profile simulation results show that the main factors controlling the deformation in the eastern part are related to the décollement of Jurassic coal beds alone, while those controlling the deformation in the western segment are related to both the Jurassic coal beds and the Eogene clay beds. The total amount of shortening from the Yaomoshan anticline to the Gumudi anticline in the eastern part is ~19.57 km as estimated from the simulation results, and the shortening rate is about 36.46%; that from the Qingshuihe anticline to the Anjihai anticline in the western part is ~22.01 km as estimated by the simulation results, with a shortening rate of about 32.48%. These estimated values obtained from the model results are very close to the values calculated by means of the balanced cross section.