The Yellow River Basin has important biodiversity protection significance. Research on the distribution hotspots of rare and endangered species can provide a basis for biodiversity protection and establishing protected area system. In this study, 70 endangered species were selected, including 26 vascular plants and 44 terrestrial vertebrates. Distribution data from multiple sources of these species were integrated to provide distribution point samples for modeling. The species distribution model Maxent was used to simulate distribution areas. All the Maxent simulation results were superimposed according to different taxa and physical geographical regions, and we calculated the biodiversity conservation value for analyzing hot spots. the conservation gaps were analyzed by integrating the distribution layer of national nature reserves and national parks (pilot area). Results show that the distribution of endangered species in the Yellow River Basin is mainly high in the south, and is concentrated in the mountain areas. The hot spots include Qinling Mountains, Taihang Mountains, Ziwuling-Liupan Mountains, Longzhong Plateau to Songpan Plateau, Qilian Mountains, Helan Mountains, and wetlands along the Yellow River. After distinguishing the geographical regions, the existing national nature reserves and national parks (pilot area) cover 13.89% of the hot spots' area, and the protection gaps are mainly found in the southern Ziwuling Mountains, the southern Liupanshan Mountains, the southern Songpan Plateau and the Laki Mountains. It is suggested that the threatened species hotspots should be taken into account in ecological conservation and high-quality development planning of the Yellow River Basin, and the natural protected area system of the Yellow River Basin should be optimized. For three different physical geographical regions in Yellow River Basin, specific suggestions are put forward:in Qinghai-Tibet Alpine Region, the protected areas should be optimized and biodiversity survey should be strengthened; in Northwest Arid and Semi-arid Region, lakes in Ordos Plateau are worthy of the enhanced protection; in Eastern Monsoon Region, the leopard, great bustard and Baer's pochard should be considered as key species and put more efforts on their habitat protection. In addition, this study also shows that, when analyzing biodiversity hotspots, considering the division of physically geographic regions and combining the hot spot analysis results of multiple taxa and single taxa for overall consideration may be better for meeting the needs of biodiversity in-situ conservation.