The research aims to systematically and comprehensively understand the diversity of rare, endangered and national key protected plants in the middle and upper reaches of Bailong River in Gansu, and analyze their phytogeography. Combining line transects survey and plot survey, and referring to relevant literature, the rare and endangered plant resources in this area were sorted out and analyzed. The results show that: (1) there are 93 rare and endangered species in this region, belonging to 25 families and 55 genera. Among them, 47 are national key protected plants, 37 are Chinese endemic species, 65 are listed in the China Biodiversity Red List (Higher Plants), 81 are IUCN Red List species, and 60 are included in the Appendices of CITES. (2) In terms of floristic analysis, the distribution patterns of families can be divided into 6 types and 4 variants, while those of genera can be classified into 10 types and 4 variants, with the highest proportion of north temperate elements. (3) Most of the 93 rare and endangered species are scattered, while a few are distributed in blocks or patches, such as Herminium monorchis, Orchis chusua, Kingdonia uniflora, etc. There are 11 species only distributed in Diebu, 45 only in Zhouqu, and 37 in both areas, with richer species in Zhouqu. The rare and endangered plants in the middle and upper reaches of Bailong River are rich in species, characterized by dominant temperate elements, transitional features from north subtropical to warm temperate zones, and rich Chinese endemic components. There are 56 species of Orchidaceae, accounting for 60% of the total. However, most of the rare and endangered species have a narrow distribution range and a small number of populations, which poses a serious challenge to their protection.