Based on the annual runoff variation characteristics in typical basins of northern regions of the Qinling Mountains from 1955 to 2010,the paper used Mann-Kendall test and ordered cluster analysis to reveal the mutation characteristics of the region's annual runoff series. The results showed that the annual runoff of Bahe river, Dayuhe river, Fenghe river, Laohe river and Heihe river had downward trend for 56 years, and the change of annual runoff modulus had synchronism from 1955 to 1983, the synchronism is poor after 1983.Except that Dayuhe River has no mutation point, the mutation point of annual runoff series in other four basins took please in the late 1980s.The result can provide reference for the development and utilization of water resources.