The paper analyzed the variation characteristics of low water flow at mountain area of Hotan river by use of the method of moving average, Mann-Kendall test and the wavelet analysis, based on monthly flow data of two tributary of Hotan river during the period of 1957to 2010. The results indicated that the change trend of low flow was not significant before the late 1990s, and low flow showed an obvious increase after the late 1990s. However, Low flow of the two tributary of Hotan river showed no abrupt change. In addition, periodicity of low flow is not significant, and the 10to 12year period of flow of the driest month is obvious. The results were mainly correlated with rising temperature and reservoir regulation.