In order to solve the problems of the unclear sedimentary patterns and uncertain control factors of sedimentary evolution of the Middle-Upper Jurassic in the southern margin of the Junggar Basin, the vertical sequence, sand body superposition mode, hydrodynamic conditions, sedimentary system evolution and control factors were analyzed by means of fine dissection of several sections and detailed sedimentary description of outcrops in the field. The research shows that braided river sediments, river sediments and fan delta sediments of Middle-Upper Jurassic were deposited from bottom to top, and the changes in hydrodynamic conditions caused by paleoclimate and tectonic events are the main controlling factors of the sedimentary evolution. Specifically, at the bottom of the Toutunhe Formation, braided river sediments were deposited in a warm and humid paleoclimate, forming a stacking pattern of stacked sand bodies; in the middle, braided-meandering river sediments were deposited when the paleoclimate began to be initially arid, forming tightly superimposed sand bodies; and in its upper part, meandering river deposits were developed and isolated channel sand bodies were formed under the condition of less rainfall and paleoclimate drought. As to the Qigu Formation, seasonal meandering river sediments were deposited under arid paleoclimate conditions; the lateral migration sand bodies were developed when the rainfall was sufficient during the wetting period; and laterally continuous sand bodies were developed during the dry period. The Kalaza Formation fan-delta sediments were deposited under hot and dry paleoclimate and intense tectonic activities. The detrital channel formed a vertical cutting sand body in the delta plain, while its frontier underwater distributary channel formed a lateral cutting sand body.