Abstract: The centrifuge shaking table tests are conducted to investigate the dynamic response characteristics of large underground structures with piles, such as underground transportation systems, under seismic loading. In addition, the potential hazards like ground liquefaction and structural buoyancy are examined. The saturated soft clay is used as the foundation soil in the tests, which are designed to represent three scenarios: free field condition, integrated shallowly-buried underground structure, and equivalent single-cell shallowly-buried underground structure. To eliminate the boundary reflection effects, a layered shear box is utilized. The horizontal seismic tests are conducted at 50g centrifugal acceleration. The test results indicate that different structures amplify the response at specific frequency bands associated with their natural vibrations. Under the premise of the equivalent overall mass, static buoyancy and moment of inertia, the integrated structure reduces the effects of the natural vibrations during seismic events compared to the single-cell configuration and exhibits superior post-seismic buoyancy resistance properties.