[Objective] Characteristics of water pollution in the Tokto section of the Yellow River and selection of water quality evaluation index is of great importance for assessing the the water quality in the Tokto section.[Methods] Based on the data of 9 sampling sections in the Tokto section from April to August in 2017, we comprehensively evaluated the water quality by establishing the evaluation index system using principal components analysis.[Results] ① The water quality in the Tokto section could be classified into class Ⅳ, and the main pollution factors are total nitrogen, total phosphors, chemical oxygen demand, belonging to organic type and eutrophication pollution.② The water quality from upstream to downstream was becoming better The water quality of the Heihe River at the entrance of tributary became worse due to the excessive pollutant discharge into Heihe River during flood season. The water quality was the worst in August and April, and was better from May to July.[Conclusion] The water quality evaluation method based on the principal component analysis and the synthetic water quality index can not only accurately reflect the water quality, but also compare the water quality of different sections. The water quality in Tokto section of the Yellow River is poor(the whole class Ⅳ), which belongs to organic pollution and eutrophication.