In view of the defect that the traditional safety evaluation method of aqueduct ignores the dynamic change of index weight and cannot reflect the impact of danger factors on the actual operating state of aqueduct in real time, a comprehensive evaluation method of aqueduct safety based on the dynamic weight-cloud model is proposed, in which the dynamic weight model is introduced to dynamically weight the evaluation index, and the cloud model is used to obtain the membership degree of evaluation index. This method was applied to the safety evaluation of the M River aqueduct in the middle line of the South-to-North Water Diversion Project and compared with the research results of static weight model. The results showed that the dynamic weight model realized that the calculation result of the weight of evaluation index layer changed in real time with the project operation state, and at the same time had a higher sensitivity to the identification of risk factors, which improved the applicability and accuracy of the evaluation method for the comprehensive evaluation of aqueduct safety under complex operating environments.