Based on the analysis of observed runoff data, annual distribution of runoff series from Hotan River is high concentration and yearly variation is small with an unnoticeable decrease trend, and the runoff series flowing into the Tarim River is concentrated in summer and yearly variation is vary large with an obvious decrease trend. The runoff in 2007and 2008from the headstream is closed to yearly mean value, but the amount of water flowing into the Tarim River decreases in large quantities. The main reasons are that the small runoff and flood in flood season, the regulation of the Wuluwati reservoir and out-of-order water diversion in the oasis irrigation area.