:As the origin of the Yangtze River hydrological cycle, the source region of Yangtze River has many important functions of ecosystem services. The changes of water quality and amount together with the unreasonable human activities in the source region have important effects on the sustainable utilization of the water resources in Yangtze River basin. Therefore, researches on the water functions, water environment capacity and control of sewage and pollutant emissions have vital significance for the management of water functional zone. In view of the water quality target of water function area and according to the monitoring data of hydrology and water quality, the pollutart carrying capacity and total limit discharge of pollutants in Tongtian River and the source region of Yangtze River in Qinghai province were studied with the aid of one-dimensional water quality model. Results show that firstly, the pollutant carrying capacity for COD_Cr and NH₃-N of National Nature Reserve of Three Rivers Source was considerably higher than that of other four water function areas including the reserved area of Nieqiaquzhiduo in status year. The pollutant carrying capacity for COD_Cr and NH₃-N of the reserved area of Nieqiaquzhiduo was the highest in planning year. However, the total control amounts for COD_Cr and NH₃-N of the Nieqiaquzhiduo reserved area were higher than those of National Nature Reserve of Three Rivers Source and Chengwenxiqunchengduo reserved area in both status year and planning year. This study could provide theoretical basis for the management of water functional zone and the eco-functional regionalization of the source region of Yangtze River.