[Objective] The variation characteristics and long-term trends of Hutubi river were analyzed for providing theoretical support for the development, which is the strategy of supply and demand balance of water resources in Hutubi area of Xinjiang Wei Autonomous Region. [Methods] The measured data of daily runoff from Shimen hydrological station of Hutubi river during 1978-2011 were analyzed by using the methods of coefficient of variation, anomalies accumulation, Man-Kendall nonparametric rank correlation test and continuous complex Morlet wavelet transform. [Results] Changes in the Hutubi river runoff during the year was mainly affected by precipitation and temperature. Its main runoff derived from May to September, and its flood season from June to August accounted for 69.4% of the annual runoff, the low flow season was from December to March of the next year. Hutubi river average coefficient of variation was 0.149 during the 34 years.The annual runoff overall showed slight increasing trend. The annual runoff variation of Hutubi river was small, its continuous low water was almost identical with the duration of the wet among years. Besides, there were four more significant cycle fluctuations of the runoff. The 18-year was the first main cycle of runoff change, and the 29-year was the second.[Conclusion] In recent 34 years, the runoff was increased in Hutubi river. At the same time, the interannual variation of runoff showed obvious periodicity. In addition, the runoff annual distribution was serious uneven.