The cable-stayed bridges (CSBs) with high-low towers have obvious asymmetry in structural layout and mechanical behavior. The stiffness and vibration mode of CSBs with high-low towers are obviously different. In order to optimize the mechanical performance of CSBs with high-low towers, taking the Shunxing Bridge with the main span of 626 m as example, a design optimization study is carried out from the suitable structural system, the ratio of side span to main span, and the setting of auxiliary piers. The results show that temperature load is a key factor in determining the unconsolidated system of the CSB with high-low towers, and it is also related to the height of the lower pylon. A reasonable ratio of side span to main span can decrease the static and dynamic response of the CSB with high-low towers; The setting of auxiliary pier can increase the structural rigidity and greatly reduce the stress and vertical deformation of the main beam on the side span. The research results can provide reference for the design of long-span CSB with high-low pylons.