///The tectono-depositional coupling relationship between the Tarim Basin and the South Tianshan Mountains has become one of the hotspots for geological research in China. This paper applies the(U-Th)/He ages of apatite and zircon from the drilling samples in the basin to study the coupling relationship between the Tarim Basin and the South Tianshan Mountains. Based on the results, the evolution model is proposed to show the tectonics-sedimentation coupling relationship between the North Tarim Basin and the South Tianshan Mountains. During Late Miocene, the South Tianshan Mountains began to uplift rapidly with serious erosion while the North Tarim Basin was dramatically subsided accepting the sediments from the South Tianshan Mountains. The He ages of apatite and zircon effectively record the geological information and provide new evidence for the study of the basin-mountain coupling relationship.