In order to promote the intelligent and automatic development of optimal design of U-shaped aqueduct, a structural optimal design system for the U-shaped aqueduct was proposed, which combines the parametric finite element program and the intelligent optimization algorithm. Firstly, based on the large-scaled finite element program HSNAP, a parametric modelling module was developed for establishing 3D parametric model of aqueduct. Then, the paralleled whale optimization algorithm was implemented with the multi-core parallelization technology for the optimization. Taking a U-shaped aqueduct project as an example, under the condition that the strength and geometric constraints of aqueduct were satisfied, the geometric parameters of aqueduct were optimized with the minimum amount of concrete as the optimization objective. The results show that the optimized scheme can meet the safety requirements of the structure and has significant economic benefits compared with the original design scheme.