<p>Earthquake-induced liquefaction often leads to foundation failure, and post-earthquake aftershocks may lead to re-liquefaction of soils. In this study, two series of shaking table tests were performed to investigate the seismic responses of composite caisson pile foundation (CCPF) and caisson foundation (CF). Each series of tests involved seven shaking events with three different peak accelerations (PA) of 0.15g, 0.30g, and 0.50g. The excess pore water pressure and settlement of the sand, as well as the acceleration, settlement, and displacement of the foundation, were compared for each shaking event. The test results show that increasing soil compaction caused by repeated seismic events may increase the acceleration response of both the foundation and superstructure, even for the events of the same PA. In a strong earthquake scenario, the peak horizontal displacement of the CCPF superstructure is essentially the same as for the CF superstructure, and the post-earthquake deflection displacements and settlement of CCPF are about half that of CF. For seismic wave inputs with different PAs, there is a linear relationship between the relative compaction of soil and the settlement and deflection displacement of the foundation. The results indicate that the CCPF exhibits superior seismic performance compared to CF. However, the squat caissons (with a smaller height-to-width ratio, H/D) enhance the inertial forces and overall flexibility of the CCPF, which in turn amplifies the acceleration effect and exacerbates the shaking of the superstructure. Therefore, the influence of these inertial forces should be accounted for in the design and testing of caisson foundations, to ensure the stability of both the foundation and the superstructure.</p>