Abstract: Natural riverbed overburden is often composed of stratified deposits of various soil types, resulting in a complex structure commonly accompanied by clay interlayers. This study conducts a series of centrifuge shaking table model tests to investigate the effects of a impermeable interlayer on excess pore water pressure, acceleration response, and spectral characteristics of sandy overburden. The results show that the sand models prepared by layered compaction exhibit enhanced liquefaction resistance under repeated shaking. The liquefaction susceptibility of shallow sandy layers is influenced by both the thickness of the overburden and the presence of a clay interlayer. The presence of the clay interlayer reduces surface acceleration response, and a significant decrease in amplification coefficients at the interlayer indicates the attenuation effect of material damping on seismic wave propagation. Although the clay interlayer can dissipate high-frequency seismic energy and attenuate low-frequency responses—thereby narrowing the plateau region of the response spectrum, reducing the maximum dynamic amplification factor, and lowering the risk of earthquake-induced structural damage—current seismic design codes may still underestimate the amplification effect of thick overburden in actual ground motion responses.