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We identified a Neogene rapid uplift-denudation event of the South Tianshan based on apatite (U-Th)/He and apatite fission track (AFT) ages in Tertiary rocks of the Tarim basin, using borehole samples. The (U-Th)/He thermochronology can be used to reveal the tectono-thermal events with lower temperature than that of AFT thermochronology and has not been used previously to study the uplift of the Tianshan Mountain. Using these data, we show the relationship between the uplift of the South Tianshan and the subsidence/deposition of the northern Tarim basin during the Neogene. The apatite helium ages reveal the migration of uplift, erosion and deposition in the northern Tarim basin. A rapid uplift of the South Tianshan during the Miocene and a corresponding rapid subsidence in the northern Tarim basin occurred. However, in the Pliocene, the Kuqa Depression and South Tianshan uplifted and eroded at the same time and in turn provided the detrital source rocks for the Northern Uplift of the Tarim basin. In contrast to earlier studies, we arrive at the conclusion that the South Tianshan experienced rapid uplift in the Miocene based on (U-Th)/He data of apatite obtained from borehole samples collected in the Tarim basin itself, and not from the bordering mountain chain. Combined apatite (U-Th)/He and fission track thermochronometry enables reconstruction of thermal histories of sedimentary rocks between 40 and 120°C, and this has implications for the generation of liquid hydrocarbon in the 65-120°C range in the basin. Thermal and burial histories of typical samples were also modelled to show the rapid uplift in our study. Our works not only provide a new evidence for the South Tianshan uplift but also indicate that there is a coupling between uplift and subsidence in the South Tianshan and adjacent northern part of the Tarim basin, which controlled hydrocarbon accumulation in the Kuqa Depression and Northern Uplift of the Tarim basin. [ABSTRACT FROM AUTHOR]