This paper adopts the fluid–structure coupling algorithm based on the acoustic fluid element, the fluid dynamic artificial boundary, and the consistent viscoelastic artificial boundary of solid media to establish a finite element model of the dynamic interaction of the reef-island–seawater system. Then, a numerical simulation of the seismic response of the reef-island site is carried out to study the seismic ground motion distribution patterns of the reef–seawater site and the reef-island–lagoon site. The innovation of this article is that the influence of reef–island topography and fluid–structure coupling is considered in the analysis when vertical ground motion is input. The results show that the slope angle of the bottom layer has a significant influence on the peak ground acceleration distribution and peak size on the island slope surface and the reef platform. For high-frequency input motion, a smaller reef platform width will induce a larger peak acceleration response on the reef platform. Seawater has a significant suppressive effect on vertical ground acceleration. The more high-frequency components of the input bedrock motion, the more obvious this suppression effect will be. The existence of the lagoon will amplify the maximum peak acceleration on the reef platform. According to the calculation results, lagoon terrain can amplify the maximum horizontal and vertical peak accelerations on the reef platform by about 19 and 6 times relative to the free-field results, respectively.