In order to adapt to the construction of long-span aqueduct in inter basin water transfer project, on the basis of digesting and absorbing the construction experience of continuous beam bridge, the aqueduct of Shulu main canal crossing the Yangtze-to-Huaihe River water diversion is selected as the continuous beam bridge aqueduct with variable cross-section continuous beam bridge as the supporting structure. After comprehensively considering the effects of structural self-weight, water load, temperature stress, prestress and seismic load on the continuous beam bridge aqueduct, the safety analysis of the main beam, pier and pile of the aqueduct supporting structure is carried out by using Midas civil three-dimensional finite element software. The analysis results show that the continuous beam bridge aqueduct structure of Shulu main canal is safe and reliable under the above loads.