In seismic regions, many underground structures are inevitably partially embedded in liquefiable sites, which may cause complex seismic response mechanisms due to the varying distribution of liquefiable soil layers. This study investigates dynamic interaction between underground structures and liquefiable soils employing three-dimensional nonlinear finite element models. The seismic response of both standard and connection sections of the subway station-tunnel of underground structures in liquefiable sites is evaluated to reveal the seismic response patterns of the soil-structure system under different liquefiable soil distribution forms. The results revealed that compared to homogeneous liquefiable sites, liquefiable interlayer sites can cause greater seismic damage to underground structures, potentially leading to failure along the entire length of the subway station. Therefore, the post-earthquake failure modes of the structure and site should be comprehensively considered based on the site layers distribution characteristics.