Masonry arch aqueducts, as important hydraulic structures, constitute an meaningful part of old irrigation infrastructures in China. The constituent materials deteriorate over time, caused by weathering processes and the defect development, influences the mechanical performance of these structures. The paper presents a comprehensive approach to evaluate the structural safety of an old masonry aqueduct with uncertain mechanical parameters and unknown geometric dimensions. This approach employed the 3D terrestrial laser scanning (TLS) to measure the geometric dimensions, and the discrete element analysis (DEM) to analyze the current operational behaviour state of the masonry aqueduct. As a case study, the Zhaimen masonry arch aqueduct in the famous Red Flag Canal, operating for more than 50 years, was investigated in this study. Obvious defects, such as the continuous loss and falling of mortar and the arch ring detaching, appeared in this old aqueduct. The TLS measurement information was used to construct a DEM model. Then this numerical model was applied to analyze the current performance of the exiting masonry arch aqueduct. The results show that the upper structure and the supporting structure can still be stable assuming that the mortar with no bond strength. In other words, the deterioration of the mortar, due to natural weathering and Calcium ion dissolution caused by natural environment and leakage, would not have a fatal impact on the structural safety. The proposed structural diagnosis and performance assessment approach can provide a reference to safety evaluation for similar masonry arch aqueducts.