Source area of Changjiang River is located at Qinghai-Tibet Plateau with severe climates. Due to technical limits, there are few investigation and reports about the unique ecological environment conditions in the source area. According to monitoring data of water quality obtained from scientific investigations in the source area in 2012, 2014 and 2015, we analyze conventional monitoring indicators and water quality indexes such as organic and metal pollutants. On the basis of the analysis, we discuss the spatial-temporal distribution of water quality in the source area in recent years. Results show that firstly, water quality of rivers in the source area are good, and water quality belongs to I type or II type in most regions; secondly, influenced by sediment contents of water body and regional geological conditions, water quality indexes vary among rivers in different regions in the source area; furthermore, water quality shows a small inter-year variation with a similar fluctuation; in comparison with the background values of other rivers in China and abroad, values of water quality in the source area are basically within the range of background values of river; finally, organic pollutants such as phthalic acid esters are detected in surface water samples of the source area. The results are important for further study on the water ecology of Changjiang source area.