Based on the monthly stream flow date of three representative hydrological stations, in the Aksu River basin during the period of 1957-2010, i.e., ShaliGuilanke station, XieHela station and XiDaqiao station, this paper calculates river inflow anomaly index and stream flow drought index (SDI). The simulation results of these two indexes were compared and the results showed that the SDI could reflect the drought situation better. Runs theory was used to analyse the SDI, getting the drought duration and droughts intensity in Aksu River basin. The results indicate that drought in Aksu River basin occurs mainly in spring (March-May). During 1957-2010, drought occurred 50 times, approximately once per year, with an average interval time of eight to nine months. After the 1990s, drought duration became shorter and intensity decreased in ShaliGuilanke station and Xi Daqiao station, but drought risk frequency and drought intensity became larger. Drought situation is increasingly grim in XiDaqiao station of China.