Abstract: This paper focuses on the seismic response of a reef engineering site under vertically incident P wave. A near-field calculation domain including reef, seawater and bedrock is intercepted and a finite element model for a reef-seawater system is established, in which the wave radiation effects of the infinite seawater domain and the semi-infinite rock foundation are simulated by the dynamical artificial boundary for fluid medium and the consistent viscous-spring artificial boundary element respectively. The theoretical solution of the free field motion of a half-space model with an overlying water layer under normally incident P wave is derived based on the medium wave theory. Then, this free-field motion is converted into equivalent seismic input loads through the seismic wave input method based on the substructure of artificial boundaries. Thereby, the P wave is vertically inputted into the reef-seawater system and the seismic analysis model of the reef engineering site is proposed. The accuracy of the present analysis model is verified through numerical examples. Furthermore, this analysis model is used to study the influences of the coupling effect of the reef and seawater as well as the wave input in the fluid medium on the seismic response of a reef engineering site. This study can provide some theoretical and methodological insight for the seismic response analysis of marine engineering.