The physical and mechanical properties of coral sand are quite different from those of common terrestrial sands due to the special marine biogenesis. Shaking table tests of three-story structures with nine-pile foundation in coral sand and Fujian sand were carried out in order to study the dynamic response characteristics of pile-soil-structure system in coral sand under earthquake. The influence of shaking intensity on the dynamic response of the system was taken into consideration. The results indicated that the peak value of the excess pore pressure ratio of coral sand was smaller than that of Fujian sand under two kinds of shaking intensities; moreover, the development speed of excess pore pressure ratio of coral sand was smaller than that of Fujian sand. The liquefaction of coral sand was more difficult than Fujian sand under the same relative density and similar grain-size distribution. The horizontal displacement, settlement, column bending moment, and pile bending moment of coral sand were smaller than those of Fujian sand, respectively. The magnification effect of column bending moment of buildings in coral sand was less than that in Fujian sand with increasing shaking intensity. This study can provide some supports for the seismic design of coral reef projects.