<p>The response of coral reefs under earthquakes is a valuable research topic. However, lateral accretion and dolomite layers, which have been confirmed to have non-ignorable effect on the seismic response of coral reefs, have been rarely discussed. In this study, we established a reef-bedrock-seawater coupling system of the Yongle Atoll in the South China Sea, incorporating both lateral accretion and dolomite layers. Quaternary reef strata were modeled as saturated poro-elastic materials, while the other strata were modeled as linear elastic solids. The dynamic interactions among various components, including reefs, bedrock, and seawater, were fully considered, and the perfectly matched layer was adopted as an absorbing boundary condition. The seismic responses, including reef flat displacement, acceleration, hydrodynamic pressure, and pore water pressure, were analyzed. In addition, the impact of lateral accretion and dolomite layers on seismic responses of reef flats was investigated. Results show that the seismic response decreased first, then increased, and finally decreased again as lateral accretion thickness grew. Increasing the thickness of shallow lateral accretion layers amplified the response, whereas increasing deep layers suppressed it. Moreover, thickening and higher dolomitization of shallow dolomite layers enhanced the response, while deeper dolomite layers mitigated it.</p>