Abstract: Eleven indicators that can represent and reflect the characteristics of cyanobacteria control engineering based on the aspects of effectiveness,reliability,safety and economy,were selected to build the indicator system and the evaluation criteria. The analytic hierarchy process was applied to determine the index weight,and the evaluation model with fuzzy mathematical method was formed. The application of environmental performance evaluation index system was tested by taking a cyanobacteria control and emergency disposal project in Erhai Lake,Dali. The index system has a clear applicability,and quantitative evaluation of the effect of cyanobacteria control,which could bescored quantitatively to assess the benefits of the cyanobacteria control project.