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The method of time series is applied to analyze the variation of precipitation and temperature from 1961 to 2002 in the mountainous areas of the Tarim River Basin, as well as water consumption in the headstream and mainstream areas. Those hydrologic parameters are verified.Quantitative results indicate that the precipitation and temperature in the headstream areas have an increasing trend to different extent. The increasing trend of precipitation is less significant than that of the temperature (α= 0.05). Runoff of three headstreams also increases especially from 1994 to 2002.Compared with the perennial runoff, the annual runoff has increased by 25.163 × 108 m3/a. However,inflows of the mainstream areas has only increased by 0.9985 × 108 m3/a. So the runoff at the different hydrologic stations in the headstream areas has a linear decreasing trend. It is shown that the degraded trend of eco-environment of the Tarim River Basin hardly changes in the special water period for ten consecutive years. Given runoff of three headstreams is accounted in normal period from 1957 to 2003,the annual runoff of the headstream areas would be only 22.57 × 108 m3. Therefore, more attention should be given to ecological safety of the Tarim River Basin.