Aimed at the investment risk which is brought from the subjectivity and randomness of owners or investors in evaluation of hydropower project scheme ,taking the four project schemes of hydropower station for example,the paper established the evaluation index system of hydropower project based on method of fuzzy comprehensive evaluation. On the basis, combining method of fuzzy comprehensive evaluation,the paper constructed membership function and fuzzy-set pair analysis which reflected the characteristics of same-indefinite-contrary system.Then it put forward the evaluation model based on analysis of fuzzy-set pair.Meanwhile,the weight of each index was determined by vatiation coefficient method.The connection degree and set pair potential were gotten through classifying plan index level of evaluation and constructing connection degree function. The paper finally gave the development trend and uncertainty rank of comprehensive level of every scheme of hydropower project so as to heighten the optimization efficiency of project scheme and reduce the investment risk of owner or investor.