The Yarlung Tsangpo River, the longest river in Tibet, houses most of the population and economy in Tibet Autonomous province. Under the rapid development of economy and society in Tibet, the pollution in the Yarlung Tsangpo River basin has rapidly increased. Evaluating water quality and water environmental capacity is needed for water resource management in Tibet. This study used a single factor evaluation method to evaluate water quality of the Zhongba-Nyingchi section of the Yarlung Tsangpo River based on measured data of COD_Cr, NH3-N and TP in the study area. Based on these data, determinations of ideal water environmental capacity, emissions of pollutants and remaining water environmental capacity of the study area were made by a one-dimensional steady water quality model under either section-head control or cross-section control. The data indicate that most of the monitoring sections in the study area experienced good water quality. The three pollutants all had large remaining water environmental capacity generally, but TP exceeded state levels in the two upstream functional areas, and levels above state standards of COD_Cr and TP were found in several calculation cells of the two downstream functional areas. Therefore, emissions of pollutants need to be reduced to protect the water environment quality of the Yarlung Tsangpo River.