The time of the uplift of the Qinghai Nanshan (the Mountains south to Qinhai Lake) is important in understanding structural evolution of the Lake Qinghai—Gonghe Basin. An angular unconformity within the Pliocene stratum was found during field exploration in northwestern part of the Gonghe Basin. Abrupt change in the detrital minerals is further confirmed by major elements and proxies of weathering intensity before and after this tectonic event, suggesting that the underlying and overlying sediments have different provenances. Combined deformation of sediments and regional information, it can be deduced that an existed thrust, Qaibeiyuan—Qinghai Nanshan northwest dipping thrust was reactivated along the region of the southward rangefront of modern Qinghai Nanshan by Late Cenozoic rightlateral movement of Wenquan fault. The mountains range is thus a tectonic ramp that thrusted southward over the Gonghe basin. The movement of Qinghai Nanshan changed the geomorphology of the basin and the sediments in the southward rangefront were tilted to southwest. After the unconformity, the Qinghai Nanshan has served as a watershed boundary and then became a new provenance of the Lake Qinghai and Gonghe Basin.