[Objective] To evaluate the current eutrophication state and provide basic data and theoretical support for the pollution control in Heihe River basin.[Methods] The total nitrogen (TN), total phosphorus (TP), permanganate index (COD_Mn), chlorophyll a (Chl.a), transparency (SD) were selected as indexes for water quality evaluation, and the comprehensive trophic state index and BP neural network were used to evaluate the eutrophication of Heihe River basin.[Results] The eutrophication status of Heihe River basin was mainly in medium level of nutrition. The nutrition status index of Yeniugou and Zhangye wetland were close to mild eutrophication. The eutrophication status of East Juyanhai Lake was severe and the total nitrogen index was high. The water environment of East Juyanhai Lake should be protected in time.[Conclusion] Compared to the comprehensive trophic state index method, the evaluation results of BP neural network are closer to the actual situation, and more objective and reliable.