For more accurate basin similarity identification, suitable reference basins are selected for the estimation of water resources status in ungauged watersheds. Five typical watersheds in northern Qinling Mountains in Xi’an City, Shaanxi Province, were taken as the research objects. Nine characteristic factors from three aspects of climate, subsurface and runoff were weighted by the assignment of variation coefficient method, and the similarity between the watersheds was calculated by weighted cosine similarity and weighted Euclidean distance similarity, respectively. The calculation results were then verified by the transplantation of parameters from the Xin’anjiang model. It is found that the weighted cosine similarity is more accurate than the weighted Euclidean distance similarity, so it is more suitable for the watershed similarity calculations. The research results can provide some technical references for runoff estimation and water resources development and utilization in the region.