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A stratigraphic and structural study was carried out in the central part of the Chinese South Tianshan (STS) within a 50–100 km-wide transect centered on the Dushanzi-Kuqa road (83°–85° E). Our data elucidate the tectonic structure and evolution of the Palaeozoic sedimentary basin, document overthrust structures in the late Carboniferous-early Permian orogenic belt and suggest correlations between the western and eastern segments of the STS in Kyrgyzstan and China. We recognise a series of lithotectonic units in the study area that have different stratigraphic characteristics and were formed within (a) continental margin and slope of the Kazakhstan continent, (b) Turkestan (South Tianshan) ocean, (c) intra-oceanic carbonate sea-mounts, which at least partly evolved on top of an extinct island arc, (d) a back-arc oceanic-crust basin, (e) external deeper marine and internal shallow-marine areas of the Tarim shelf and (f) Tarim craton. The overall structure of the basin was similar within Kyrgyzstan and China. The main distinction of the western areas is a lack of ophiolites on the southern flank of the belt, a poorly expressed arc in the axial part, and a more complicated facial setting of the central area, where carbonate banks were separated by deeper marine depressions with cherty deposits. The eastern sector is defined by a continental arc that evolved on the northern margin of the Tarim craton in the Silurian and became separated from the continent in the latest Silurian-early Devonian. There is also a middle Palaeozoic metamorphic belt on the southern flank of the STS. A pre-Carboniferous unconformity, previously assumed throughout the study area, is only confirmed within the continental massifs of Kazakhstan and Tarim. As in the western areas, the unconformity does not exist within the STS. Continuous sedimentation in the STS occurred from the Early Devonian to the early Bashkirian in marginal parts of the belt and up to Gzhelian age in the axial part. Convergence began in the Bashkirian (320–315 Ma) and caused subduction of oceanic crust in the northern and southern areas of the STS to the north and south, respectively. A back arc basin in the south was closed in the Moscovian, and since that time top-to-the-south thrusting and overthrusting prevailed throughout the STS. The time of onset of collision of Kazakhstan with Tarim was not younger in age than Kasimovian, based on the age of initiation of a turbidite foreland basin on the northern margin of Tarim. Thrust deformation during the Late Pennsylvanian to early Permian was synchronous within Kyrgyzstan and China; it occurred in a collisional setting and was accompanied by accumulation of turbidites and olistostromes. Broad termination of thrusting, followed by folding and uplift of the area in the middle Asselian indicates the beginning of a rigid collisional phase. Emplacement of early Permian stitching granite plutons in the STS and adjacent areas of Kazakhstan and Tarim completes the formation of the collisional orogen within Kyrgyzstan and northwestern China.