Based on the low-flow data in 1960~2009 in the Three-River Headwaters Region (TRHR), the trends of monthly runoff and the recession coefficient in the runoff recession process were analyzed, and the low-flow process was reconstructed by the monthly runoff recession coefficient. The results showed that: (1) the monthly runoff showed a decreasing trend in the low-flow period both in the Yellow Rivers Headwaters Region (YERHR) and the Lantsang Rivers Headwaters Region (LARHR), and the trend showed a weak increase in the Yangtze Rivers Headwaters Region (YARHR). The low-flow was controlled by summer-flow, and both of them kept a consistent changing trend. (2) The runoff recession coefficient in runoff recession process showed an increasing trend both in the YERHR and YARHR, which means that the runoff recession process was slowed. This is due to increasing groundwater capacity under long-term climate warming. The trend of runoff recession coefficient was not obvious in the LARHR. (3) the winter (from November to February) runoff recession process can be reconstructed by mean monthly runoff recession coefficient and the runoff of October in the TRHR with high simulation accuracy, the difference between the calculated and observed value were less than 8%. The study can provide beneficial reference for understanding the characteristics of low-flow under the background of climate change and hydrologic forecasting in the Three-River Headwaters Region.