To investigate liquefaction behavior in deep liquefied soil layers, this paper performed shaking table tests using three seismic waves, i.e., the Ming Shan wave, Beijing Hotel wave and Beijing artificial wave, as the dynamic loads. By comparing free-field and structural conditions, the liquefaction characteristics of deep liquefied soil layers were analyzed. For the soil layer, no water spraying and sand bubbling occurred on the surface, but cracking developed near the structure. The pore-pressure ratio in the free-field condition was much smaller than that in the structural condition. The pore-pressure ratio induced by the Beijing Hotel wave was the largest, followed by that induced by the Beijing artificial wave and then the Ming Shan wave. For the structure, the Beijing Hotel wave produced the largest structural acceleration and the greatest increase in tensile strain, followed by the Beijing artificial wave and then the Ming Shan wave. These results indicate that liquefaction of deep liquefied soil layers is mainly controlled by overburden stress and the frequency content of the seismic wave: larger overburden load and higher dominant seismic frequency both reduce the degree of liquefaction. The seismic response of the station structure correlates closely with the dominant seismic frequency.