In order to connect a reservoir to the water system of an inner lake in a planned residential district, as well as pass through an urban first-grade highway, a box-culvert structure will be built under the highway. The larger cross-section of the box-culvert in the preliminary design is on the conservatively safer side but not as economical, and yet will cause excessive foundation deformation due to heaver self-structural load. This paper proposed an optimal design with the best combinations of sidewalls, floor, and roof thickness of the box-culvert structure. Finite element method analysis of the stress and deformation of the box-culvert structure and its foundation with the highest and lowest water table levers during its simulated construction period was conducted. As a result, an optimal design was concluded, which not only reduces the use of concrete, but also reduces the demands on the bearing capacity of the foundation soil.