Sandy silt seabeds are susceptible to liquefaction under the influence of larger wind waves, posing a threat to seabed stability. This study investigates the dynamic response of sandy silt seabeds through model experiments conducted in a wave flume under varied wave heights, periods, and water depths. The research combines experimental data and theoretical analysis to explore the development of pore water pressure, liquefaction processes, and seabed soil stratification induced by wave loading. The results reveal that larger wind waves induce the accumulation of transient oscillatory and residual pore water pressure in sandy silt seabeds. The amplitude of pore water pressure increases with higher wave heights and longer wave periods lead to larger amplitudes of oscillatory pore water pressure. The wave-induced liquefaction processes vary based on different wave conditions and initial stress states. Additionally, experiments reveal a suspended particle-enriched zone in sand wave-affected areas, contrasting with less apparent accumulation in areas without sand waves. Sediment particles overflow from the seabed in both cases. In the substrate layer (0–4 cm below the seabed surface) of the areas affected by sand waves, sediment particle size decreases with depth. In non-sand wave areas, the seabed surface exhibits sinusoidal vibrations, with larger particles at 0–1 cm depth, and increasing particle size with depth from 1 to 4 cm below the seabed. This comprehensive investigation provides valuable insights into the complex dynamics of sandy silt seabeds under wave loading, offering crucial information for engineering applications.