River piracy has been reported worldwide and was regarded as one of the main drivers for landscape evolution. In this study, we introduce an example of river piracy in the northern Qilian Shan (northeastern Qinghai-Tibet Plateau), and further interpret its regional geomorphological implications. Chi-map analysis, erosion potentiality evaluation, and river profile inversion are used to verify the river piracy. The results confirm that the transverse river, the Hongshuiba River, has captured the longitudinal river, the Zhulongguan River at ~0.35 Ma, due to the headward-migrating erosion of the main stem of the Hongshuiba River. The drainage reorganization, with longitudinal rivers captured by transverse rivers, is a common and continuous landform process along with the outward growth of the northern Qilian Shan. Moreover, the present Qilian Shan watershed geomorphic system could be considered as a transient stage of drainage evolution during the mountain building. •The Hongshuiba River has captured the Zhulongguan River at ~0.35 Ma•River piracy is common phenomenon in northern Qilian Shan•The present Qilian Shan topography is in a transient stage of drainage evolution during the mountain building.