Submerged horizontal plates can resist waves while allowing water circulation, and seagrass beds serve to purify water, sequester carbon, and protect shorelines. This study proposes an ecological breakwater design that integrates seagrass beds planted on submerged horizontal plates. Using the smoothed particle hydrodynamics (SPH) method, a numerical wave flume was established. The reliability of wave interactions with permeable media and submerged horizontal plates was validated through numerical reproduction of physical experiments reported in the literature. The calibration of median particle diameter parameters for the permeable media model, which substitutes for the seagrass bed, was also conducted. Based on this, the wave transmission and reflection coefficients of the ecological breakwater were investigated under varying seagrass bed stem densities, seagrass bed heights, horizontal plate submergence depths, and wave heights. Results indicate that planting seagrass beds enhances the wave resistance capacity of submerged horizontal plates. Increasing seagrass planting density and relative height, reducing the relative submergence depth of the horizontal plate, and utilizing the breakwater in areas with larger relative wave heights all contribute to improving the wave dissipation performance of the ecological breakwater.