The Sino-Himalaya region is located in the southeast margin of the Qinghai-Tibetan Plateau (QTP) with several Asian rivers in this area, namely the Yarlung Zangbo River (YZR), Salween, Mekong, and Jinshajiang River and their tributaries. All these rivers currently flow independently into the Indian Ocean, the South China Sea (Pacific Ocean) and the East China Sea (Pacific Ocean). In geologic history, however, these rivers flowed southward into the Paleo-Red River (PRR), forming a huge drainage system, which then flowed into the South China Sea. From the end of the Neogene to the beginning of the Quaternary, with further uplift of the QTP, the monsoon climate was formed and strengthened bringing abundant precipitation leading to river erosion, rapid undercutting and a series of river capture events resulting in modern drainage systems and the beheading of the huge PRR. The reorganization of the PRR led to changes in the spatial pattern of river systems, subsequently affecting the geographical distribution of plants in the river valley. This paper reviews the effects of drainage evolution on the genetic structure and geographical pattern of plants in this region, and summarizes the resulting four types of discontinuous distribution patterns observed, namely: (1) the discontinuous distribution pattern between the Three River Valleys (TRV) (Salween, Mekong, Jinshajiang and their tributaries) and the Red River Basin (RRB); (2) the discontinuity between the Yarlung Zangbo River and the TRV–RRB; (3) the discontinuity among the TRV, and (4) the discontinuity between the east and west ends of the QTP. The conclusions from this review, while providing botanical evidence supporting and confirming the drainage evolution in Sino-Himalaya China, are the following: (1) the reorganization of drainage systems made the original continuous distribution pattern discontinuous, forming unique genetic and biogeographical characteristics, promoting the genetic differentiation of species and the formation of new taxa; (2) river capture events link different river systems together, bringing together the genetic diversity of different river valley species, increasing the richness of genetic diversity and the exchange of genes among populations; (3) the reorganization of river systems impacts the evolutionary history of valley plants and shapes their modern distribution patterns.