The Qinghai Nanshan is located interior of northeastern Tibetan Plateau, extending W-E trending for 200 km between the Ela Shan and Riyue Shan, constituting the northern boundary of the Gonghe Basin. Qinghai Nanshan is very important to understand the Qinghai lake Basin-Gonghe Basin landscape evolution process, and it also provides a clue to understand the deformation of northeastern Tibetan Plateau. Our study focuses on identifying the unrecognized segment of the Qinghai Nanshan fault along the Gonghe Basin by applying river longitudinal profiles, and geomorphic indices such as stream length (SL) gradient index and mountain front sinuosity (Smf), as well as combining the field investigation. The results show that the anomalies of river longitudinal profiles in their upper reach may result from lithological contact, whereas the pronounced convex and deflection that occurred especially in the mid-reach are most likely related to recent tectonic activities caused by the Qinghai Nanshan thrust fault. Moreover, SL values are in agreement with the anomalies shown by the longitudinal profiles. Combining the results of geomorphic indices and topography analysis, as well as the field investigation, we project the distribution of the Qinghai Nanshan fault and discussed the tectonic implications. The listric Qinghai Nanshan thrust fault and the influences from the Elashan and Riyueshan dextral strike-slip faults are controlling factors for landscape of the Qinghai Nanshan.