By use of monthly precipitation data measured in three headstreams of Tarim River in recent 50 years, this paper analyzed the multi time scale variation characteristics of drought flood index in virtue of the methods of nonparametric test and wavelet transforms. The results indicated that: ① the drought-flood indexes are presents the apparent increasing trend in Aksu River and Yarkand River, and the insignificant rise in Hotan River. ② The drought-flood indexes of the three headstreams took place remarkable mutation in 1986. ③ There are significant periods of 4 and 8 years for drought-flood indexes of Aksu River and Hotan River, and there are that of 8 and 10 years in Yarkand River. The results can provide a scientific basis for the reasonable utilization of water resources in the Tarim River basin.