The Gonghe Nanshan fault is a major accommodating fault within the rhombic block located between the Qilian—Haiyuan and the East Kunlun Faults on the northeastern margin of the Tibetan Plateau. However, studies on the fault activity since the Late Quaternary are limited. This study investigates the geometric distribution, activity timing, and vertical slip rate of the southern margin fault of the Gonghe Nanshan, the largest fault of the Gonghe Nanshan fault system, through high-resolution satellite image interpretation, unmanned aerial vehicle aerial surveillance, field geological and geomorphological investigations, and chronological analysis (¹⁴C and optically stimulated luminescence dating). The results show that the fault generally strikes NW-EW and is dominated by compressional thrusting. It has remained active throughout the Late Quaternary, with the most recent activity in the western segment occurring at the end of the Late Pleistocene and notable activity on the middle-eastern segment during the Middle Holocene. Combined with mountain elevation profile analysis, the vertical slip rate of the fault is overall low and segmented: (0.17±0.06) mm/a for the western segment and (0.32±0.15) mm/a for the middle-eastern segment. These results indicate that the overall uplift-related stress in the Gonghe Nanshan range is concentrated in the central arc of the mountain. By combining previous research with this study, the southeastern Gonghe Basin is inferred to have developed as a piggyback basin controlled by the Gonghe Nanshan thrust fault zone, sharing similar characteristics with the Qinghai Lake Basin.