Based on the runoff data of the Three-River Headwaters Region ( TRHR)between 1960 and 2009, numerical analysis was coducted through the digital filter method,and the Depuit-Boussinesq equation was used to calculate the recession coefficients. At the same time,the Mann-Kendall trend test method was used in runoff trend analysis. The results showed that: ( 1)In the past 50 years,discharge of the Yellow Rivers Headwaters Region ( YERHR)and the Lantsang Rivers Headwaters Region ( LARHR)significantly decreased,but no obvious discharge change was found in Yangtze Rivers Headwaters Region ( YARHR). ( 2)The runoff of the dry season in the TRHR was mainly controlled by the base flow. The ratio of the base flow to the winter runoff could be up to 100%. Base flow of YERHR and LARHR were declining in past 50 years,and Their variation trend and the sudden change point of the base flow are consistent with the runoff. ( 3)Upon the climate change effects, precipitation was the main factor that influenced runoff and recession processes in TRHR. The precipitation increasing of could lead to the decrease of the recession coefficient,while the influences of temperature on the water recession processes in TRHR were uncertain. This study provides a theoretical reference for the evolution of the TRHR runoff processes responding to climate change.