Aqueduct is an important long-distance water conveyance structure in the South-to-North Water Diversion Project, and its operation safety is crucial to the stability of the whole trans-basin water conveyance system. Aiming at the aqueduct performance evaluation, based on the modeling and analysis results of the monitoring data of an aqueduct, a comprehensive evaluation method of the aqueduct safety based on the fusion of the cloud model theory and the prediction and analysis results of several monitoring points was proposed by the cloud model and data fusion method commonly used in the study of uncertainty problems. When evaluating the performance of an aqueduct, this method relies on the analysis results of the aqueduct safety prediction model, which effectively avoids the subjectivity of the evaluation process. Experimental results show that this method can accurately evaluate the working behavior of the aqueduct according to the analysis results of the prediction model, so it can provide a new approach for the comprehensive safety evaluation of aqueducts.