Abstract Building-up of the modern Tian Shan range due to the India-Eurasia collision induces the flexural subsidence of the southern Junggar block. The sedimentary infill and subsidence in the southern Junggar foreland basin recorded the growth of the northern Tian Shan. We analyze four seismic profiles, well logging data, and trends in stream morphology in the foreland basin to decipher its architecture, and stratigraphic and subsidence history. The southern Junggar foreland basin system can be divided into the northern Tian Shan wedge-top, Lakes Aiby-Fangcao-Baijiahai foredeep and Luliang forebulge and backbulge depozones. The seismic profiles present the active shortening structures in the wedge top and the northward thinning and onlapping Neogene-Quaternary foreland sequence in the foredeep. The growth strata and unconformities separating the growth and pregrowth strata in the upper part of the foreland sequence are identified in the wedge top depozone. This indicates that the competition between active local folding relief and regional bedrock subsidence determines erosion versus deposition in the wedge top. The logging data of well GQ2 reveal that the present wedge-top depozone evolved from distal lake sedimentation, probably in a foredeep setting, to a braided river in a modern piedmont setting. These lines of sedimentary evidence and the active shortening structures reveal the northward migration process of the southern Junggar foreland basin driven by the northward propagation of the Tian Shan since the Neogene. The north-northeast dipping topography of the northern Tian Shan thrust wedge controls the north-northeastward flowing of all the rivers in the wedge top, and these rivers’ flowing direction changes in the foredeep depozone where the tectonic landform flatten out. Growth of anticlines in the front of the wedge-top depozone may have triggered a northward migration of the meandering channel of the Manas river in its lower reach. The transition between the trends of the stream morphology in the wedge top and foredeep depozones suggests the control of the structures of the foreland basin system on trends in stream morphology.