The prestressed concrete drainage aqueduct on the left bank of the Middle Route of South-to-North Water Transfer Project will have no water transferred for almost a whole year while in  short flood period the flow changes greatly. It will also suffer from drastic temperature difference between the sunny side and shade side in summer. Considerations for the design of drainage aqueduct are presented, and 3D finite element calculation is performed to comparatively analyze the stresses and displacements of the aqueduct under all load cases. It’s confirmed that temperature effect on prestressed drainage concrete aqueduct could not afford to be ignored when designing the aqueduct. This research would be referential for the design and construction of similar structures.