Due to the existence of a deep seawater layer in marine sites, its influence on the seabed ground vibration characteristics and the seismic response of marine structures is significant and should not be ignored in the seismic analysis of marine structures such as cross-sea bridges. Therefore, the study firstly establishes the seismic fluctuation analysis model based on the seismic fluctuation theory for the coupled seawater-seabed-stayed bridge to determine the influence of the seawater layer on the seismic response of the structure. In addition, considering that the marine environment may pose a threat to the durability of the damping members, the study proposes a new type of cable-stayed bridge damping system using Bulking Restrained Brace (BRB) with excellent durability as the longitudinal damping member, and takes the Qingzhou channel bridge as the engineering background to verify the seismic response by comparing it with the floating system cable-stayed bridge model. The feasibility of the new type of seismic damping system considering the influence of marine environment is verified. Finally, the study optimized the location and equipment parameters of the BRB. The design method of BRB as a longitudinal damping member of cable-stayed bridge is further determined. It is found that the hydrodynamic effect generated by seawater under the seismic action will amplify the seismic response of the superstructure of the cable-stayed bridge. And by comparing the seismic response of the structure under different working conditions, it was found that the best overall seismic damping effect of the bridge was achieved when the BRB was installed at the pier and tower locations simultaneously. In addition, the parameters such as yield bearing capacity of BRB also have a great influence on the seismic performance of cable-stayed bridges.