Water resources efficient utilization is the key to ecological improvement and economic development in Tarim River Basin. It is necessary to analyze the water resources utilization and its variation tendency in the whole river basin. Based on the monitored data and formation at eight meteorological stations and fifteen hydrological stations, the method of time series, regression analysis are applied to analyzing the water resources utilization and variation trend in the headstreams and mainstream areas especially in recent 10 years. The quantitative results indicate that inflows of the headstream areas have an increasing trend to different extent in the past 40 years. The runoff increasing trend is more significant from1994 to 2002, which show the water resources condition in the headstreams is at an advantage. However, under the condition of water increase with the volume of 25×108 m3 in headstreams in recent 10 years, the mainstream water flowing from the head-streams has increased less than 0.9985×108 m3. In addition, the runoff at the different hydrologic stations along the Tarim River has a significant linear decreasing trend. It is shown that the degraded trend of ecological environment in the mainstream areas hardly changes even if the Tarim River Basin is in the special water period for ten consecutive years. Water resources efficient utilization is the key to ecological improvement and economic development in the whole river basin. It is necessary to analyze the water resources utilization and its variation tendency in the whole river basin. Based on the monitored data and formation at eight meteorological stations and fifteen hydrological stations, the method of time series, regression analysis are applied to analyzing the water resources utilization and variation trend in the headstreams and mainstream areas especially in recent 10 years. The quantitative results indicate that inflows of the headstream areas have an increasing trend to different extent in the past 40 years. The runoff increasing trend is more significant from 1994 to 2002, which show the water resources condition in the headstreams is at an advantage. However, under the condition of water increase with the volume of 25 × 108 m3 in headstreams in recent 10 years, the mainstream water flowing from the head-streams has increased less than 0.9985 × 108 m3. In addition, the runoff at the different hydrologic stations along the Tarim River has a significant linear decreasing trend. It is shown that the degraded trend of ecological environment in the Modern Areas hardly changes even if the Tarim River Basin is in the special water period for ten consecutive years.