Although China has established a relatively complete seismic design system for buildings and structures on land areas, minimal research has been conducted on seismic problems associated with marine engineering, particularly with respect to seismic response analyzes of reef sites. With the rapid development of the South China Sea in recent years, it is necessary to conduct a seismic hazard analysis during the design of reef sites. This study introduces typical engineering geological conditions and seismic activity characteristics of reef sites in the South China Sea. Through a comparison with common methods employed in site seismic response analysis at home and abroad, four critical factors and relevant solutions are proposed:(1) the terrain on islands and reefs in the South China Sea is distinct and it requires (2) specialized geo-technical engineering material; (3) the dynamic interaction between the seawater and reef should be considered; and the (4) input ground motion in the seabed of the South China Sea needs to be determined. This study provides research ideas for conducting stability analyzes of reef sites with respect to earthquakes, and also acts as a reference for seismic hazard analyzes during construction on islands and reefs in the South China Sea.