In order to enhance the water exchange capacity and improve the water quality environment inside fishing ports, a two-dimensional hydrodynamic and water exchange mathematical model was established to investigate the influence of structural parameters of seawater exchange breakwaters, including the spacing, layout range, bottom elevation, and diameter of pipe culverts. The results show that the pipe culverts can be arranged starting from areas with significant concentration differences inside the port, and their installation near the entrance can be omitted. An increase in the diameter of the pipe culverts significantly enhances water exchange, and its influence is greater than that of other structural parameters. The promoting effect of the seawater exchange breakwater on water exchange is most significant in the first tidal cycle, while its contribution rate gradually decreases in subsequent cycles. It is concluded that seawater exchange breakwaters can effectively enhance water exchange inside the port, and comprehensive design considering the optimization of structural parameters, berthing stability and investment benefits should be applied in practical engineering.