Abstract: This study focuses on the seismic response and its influencing factors of a typical coral reef island in the Xisha Islands, South China Sea. A 2D FEM numerical model was established, considering the unsaturated condition of coral sand and the topographic, geomorphologic, and engineering geological conditions of the coral reef island. The numerical model was then verified through the recorded seismic data captured by the 3-channel seismometer on the island. The influence of factors such as coral sand thickness, soil dynamic parameters, shear wave velocity of the reef limestone, and groundwater level on the seismic response of the coral reef island was systematically analyzed based on the verified numerical model. The findings are as follows:(1) As the thickness of the coral sand layer increases, the characteristic parameters of seismic response, such as the PGA amplification and the Arias intensity, also increase, and the peak value of the PGA amplification factor gradually concentrates around 1 Hz. (2) Studies on the influence of maximum dynamic shear modulus and reference shear strain on seismic response have shown that the better the dynamic characteristics of coral sand on the island, the smaller the seismic response of the island surface. (3) The shear wave velocity of the reef limestone significantly impacts the PGA amplification factor, while it has a minor effect on residual displacement and peak acceleration. (4) As the groundwater level rises, the values of characteristic parameters of seismic response gradually increase. This result indicates that the higher the groundwater level, the stronger the seismic response of the coral reef island. (5) Normalizing the influence factors has shown that the maximum dynamic shear modulus has the greatest impact on residual displacement, while the coral sand thickness has the greatest influence on peak acceleration and total Arias intensity.