By taking two typical eco-friendly wave-dissipating elements on muddy coasts, namely oyster reefs and mangroves, as research objects, a numerical simulation was conducted on the hydrodynamic characteristics of regular wave propagation and evolution over oyster reefs and mangroves based on the non-hydrostatic wave SWASH model. Furthermore, the wave dissipation variation laws of a single oyster reef, a single mangrove, and their synergy on muddy coasts under different combinations of water levels and waves were explored. The results indicate that the combined condition of oyster reefs and mangroves effectively improves the overall disaster reduction efficiency, and the wave dissipation process exhibits nonlinear variation characteristics. In the synergistic wave dissipation condition, mangroves have a significant enhancement effect on oyster reefs, and engineering layouts can prioritize increasing the planting scale of mangroves to achieve efficient disaster reduction. Under low-water-level conditions, the wave dissipation contribution rate of oyster reefs can reach more than 50%, while at high water levels, mangroves play a dominant role in wave dissipation relying on the canopy structure, and the sequential coordination of the two can achieve progressive energy dissipation and disaster reduction.