Aiming at problems of the index weighting and the operator optimization of fuzzy comprehensive evaluation(FCE)method in the aqueduct safety evaluation, a comprehensive evaluation method of aqueduct safety based on the of improved FCE method was proposed. In the proposed method, the analytic hierarchy process(AHP)method based on the natural index of e^0/5 to e^8/5 was used to obtain the subjective weight of each evaluation index, and the objective weight of the experts was calculated by entropy weight method to optimize the subjective weight. Then the total objective membership degree was calculated by introducing the all-optimal synthesis operator, and the risk degree was obtained by the weighted synthesis with the corresponding risk grade, to determine the safety category of the aqueduct. The method was applied to the safety evaluation of a specific project, and the results show that the evaluation results were consistent with those of the principal factor protruding type composition operator and the weighted average type composition operator. This method reduces the subjective deviation, avoids the selection of operators, and has strong maneuverability.