Abstract: Based on the concept of water conservation, the connotation and characterization index of water conservation function were analyzed, and the technical framework of water conservation function evaluation in the Three-River Headwaters Region was put forward. Furthermore, a hydrological model in the Three-River Headwaters Region was built based on SWAT model and was used to simulate the runoff of the Three-River Headwaters Region in diffirent time scales. The calibration results of the hydrological model showed that the maximum relative error of the daily runoff was less than 17.0%, and the maximum relative error of the monthly run off was less than 13.0%. In the daily scale simulation, the Nash efficiency coefficient (ENS) of the Zhimenda station was over 0.6, and that of the other two stations were more than 0.5. In the monthly scale simulation, ENS of all three stations was more than 0.6, which showed that the simulation results of the daily and the the monthly scale model were acceptable, and runoff process of the Three-River Headwaters Region was revealed by the developed model. The model was applied to assess the water conservation function of the Three-River Headwaters Region, the Yangtze River, the Yellow River and the Lancang River Basin water supply could be achieved respectively 158.8×10⁸, 326.2×10⁸, 72.6×10⁸ m³. Considering the impact of the land use and the vegetation change in the runoff of the river basin, the vegetation damage could have caused the Yangtze River, the Yellow River, and the Lancang River Basin to reduce the runoff of the underground runoff about 98.6×10⁸, 200.1×10⁸, 44.5×10⁸ m³. Under the condition of same climate, poor vegetation could increase the maximum daily flow of the Yangtze River, the Yellow River and Lancang River Basin about 80%, 60% and 30%. As a result, it was impotant for Three-River Headwaters Region to provide the water supply, improve the regulation capacity of runoff and relieve the flood pressure.