Former approaches for designing reinforced concrete aqueduct with multi-longitudinal beams were mostly based on experience. In this study, an optimization method is proposed instead. According to the mechanical characteristics of aqueduct, optimization principles for structural deformation coordination and sectional crack-resisting are developed. Furthermore, in optimization of large and complex reinforced concrete aqueduct, this method employs nominal tensile stress to control the maximum crack width. In addition, a 3D beam-shell element model is suggested for calculating internal force of aqueduct.