<p>Unlike common terrestrial sands, the seismic performance of densified coral sand foundations is unclear. Combining shaking table tests and numerical calculations, the seismic response and internal deformation of coral sand–raft–superstructure system with different relative densities were studied. The intrinsic particle-scale causes of variation in seismic response of coral sand due to densification were discussed. Moreover, the microscopic mechanism of the change in the dynamic stability of coral sand as foundation was revealed by comparing with terrestrial sands. The results show that the densification of coral sand foundation reduces the settlements of soil–raft–superstructure, but enlarges the acceleration and bending moment of the superstructure. Moreover, the excess pore pressure ratio of the coral sand foundation decreases with the increase of relative densities due to the stronger interlocking effect among particles. In the seismic design of coral sand foundation, it is worth noting that although the densification decreases the liquefaction potential of the coral sand foundation, attention should be paid to the amplification of the vibration response of the superstructure.</p>