The Yangtze River Basin is a priority biodiversity conservation area of global significance. To understand the diversity, threatened situation, and conservation status of the aquatic amphibians and reptiles in the Yangtze River basin, the basin was divided into 11 geographical units mainly based on the natural drainage. The cataloging method was conducted to reveal the species composition of aquatic amphibian reptile in the area. The G-F index method was used to measure regional species diversity. The weight assignment method was used to assess the species' threat status and conservation priority in the region. The result showed that 281 species were recorded in the area, including 225 amphibians and 56 reptiles. The amphibians contained 2 orders, 9 families and 37 genera, and reptiles contained 3 orders, 9 families and 22 genera. There were 119 endemic species to the Yangtze River Basin, accounting for 42.35%; 60 species are under state key protection, accounting for 22.06%; 102 species were threatened, accounting for 36.30%. The species diversity of the two taxa showed a similar distribution pattern of "Upstream high, downstream low and right bank high, left bank low". For aquatic amphibians, the Jinshajiang-Yalong sub-basin (JSYL), Minjiang-Tuojiang sub-basin (MJTJ) and Wujiang-Chishuihe-Qingjiang sub-basin (WCQ) have higher conservation priority; For aquatic reptiles, the Headwater of Yangtze River basin (JY), the Taihu sub-basin (TH) and the Middle-Lower mainstream sub-basin (ZXG) have higher conservation priority. The results indicated that the irreplaceability of aquatic amphibians and reptiles was strong in the Yangtze River Basin, the protecting attention and the protection urgency were also high. So, we suggest further strengthening the investigation of the background resources in the basin, establishing a scientific and efficient integrated protection management system for joint prevention and control, establishing and improveing monitoring and evaluation mechanism for regional species diversity, and paying attention to increasing scientific research investment and enhancing public conservation awareness. This study provides an important reference for the conservation of species diversity in the Yangtze River basin.