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There are 51 tributaries in the middle reaches of the Yarlung Zangbo River (YZR), and the confluences of 87% of the tributaries west of Jiacha Gorge are high-angle or perpendicular, reflecting the anomalous development of these tributaries. In this paper, field investigation and digital elevation model (DEM) methods were used to analyse the causes of this anomalous phenomenon, and it was found that there was a watershed in the area of the Jiacha Gorge. The palaeo-YZR west of the Jiacha Gorge flowed westward before the early Pleistocene into the Zada, Zhongba, Jilong and Gamba–Dingri palaeolakes, which featured a large amount of total accommodation space in the western Qinghai–Tibet Plateau; thus, this river was a continental river. With the intensification of the collision between the Indian plate and the Eurasian plate, the Qinghai–Tibet Plateau experienced rapid uplift and formed a landscape with high elevations in the west and lower elevations in the east, promoting the headward erosion of the eastward-flowing river. During the early Pleistocene, the river east of the Jiacha Gorge crossed the watershed and captured the palaeo-YZR, causing a reversal in the flow direction of the palaeo-YZR.