The Qilian Shan, in the northeastern Tibetan Plateau, has been continuously extending to the foreland since the late Cenozoic, resulting in the deformation of the Hexi Corridor Basins. Five terraces of the Hongshui River are faulted in the southern Zhangye Basin, a sub-basin of the Hexi Corridor, documenting the tectonic history of the Minle Fault since the late Quaternary. In this study, a high precision digital elevation model (DEM) generated by the unmanned aerial vehicle (UAV) photogrammetry is used to obtain the cumulative vertical offset of each terrace, and the abandonment ages of terraces are dated by AMS C dating. The results show that the Minle Fault has been active since the Holocene, and produced an almost constant shortening rate of 0.95±0.30 mm/a since 42.3±0.5 ka, indicating that the deformation has spread into the Zhangye Basin. Active tectonics and GPS data indicate the uniform deformation in the Zhangye Basin but different shortening rates in the eastern and western basin. The differential allocation of deformation could have been caused by different wedge structures. Deformation of the North Qilian Fold-Thrust System (NQFTS) has been uniform since the late Quaternary and may be consistent with that in 10-year timescale, although further studies are needed.