ABSTRACTThe southern margin of the Junggar Basin (SMJB) represents the typical intra‐continental basin–orogen coupling structure of the Central Asian Orogenic Belt and is a key area to study the deformation mechanisms and the geodynamic evolution processes of the North Tianshan Orogen. Herein, we compiled data from boreholes, gravity and magnetism, seismicity‐ and magnetotellurics‐derived geological profiles and field data to recover the sedimentary history of the SMJB and discuss the intra‐continental deformation driven by the basin–orogen coupling mechanism. The results show that the sedimentary and tectonic evolution of the SMJB were both profoundly controlled by the intra‐continental orogeny of the North Tianshan Orogen and its coupling with the Junggar Basin during the Meso‐Cenozoic period. Consequently, the SMJB is dominated by thick‐skinned thrust nappes accompanied with strike‐slip faulting and thrusting. The foreland thrust belt of the SMJB is characterised by three structural belts, from south to north, including the basement‐involved thrust belt, the cover‐detached foreland thrust‐fold belt and the thrusted foreland basement uplifts, respectively. Meanwhile, as indicated by the geometry of the basement thrusts, the thickness of décollements and the structure of the foreland basement, the stress field in the SMJB is obviously stronger in the west and weaker in the east. The sedimentation and deformation migrated northwards into the basin area in a stepwise process, that corresponded to the pace of the overthrusting of the North Tianshan Orogen onto the Junggar Block. Intense regional compression induced the rapid uplifting of the North Tianshan and the significant crustal shortening of the Junggar Block, driving the three structural belts to form accordingly during the Late Jurassic to the Neogene. There are at least one or two décollements within the SMJB, representing one of the main features of basin–orogen coupling structure in most cases. The décollement of some layers represents the decoupling of the sedimentary cover with the basement, which helps to accommodate the lateral crustal shortening of the SMJB by a translation into vertical uplift. As a result, the detached foreland thrust‐fold belts in the shallow level of the upper crust overthrusted upon the basement‐involved nappes of the mountain's side, forming the opposite thrust system. Coevally, the basement of the basin, in the deep level of the upper crust keeps underthrusting beneath the North Tianshan Orogen, forming a typical crocodile mouth‐like structure. In general, both the shallow and deep deformation in the SMJB have been formed by the intense intra‐continental compression during the Meso‐Cenozoic, which were driven by the basin–orogen coupling mechanism.