Abstract: In recent years, tropical and subtropical islands have faced increasing risks of tsunami due to the degradation of coral reefs and consequent decline in natural wave-dissipation capacity. Although traditional continuous submerged breakwaters can effectively attenuate wave energy, their enclosed structures tend to impede water exchange on reef flats, leading to water level elevation and seabed erosion. To address these issues, this study proposes a segmented submerged breakwater configuration adapted to coral reef topography, which is composed of discontinuous solid units and gap areas to maintain wave attenuation performance while optimizing water exchange. Through physical model experiments in a wave flume, we systematically investigated the mechanisms by which segmented submerged breakwaters influence the dimensionless maximum wave height, reflection coefficients, transmission coefficients, and maximum wave run-up height during solitary wave propagation. The results show that the presence of the segmented submerged breakwater significantly affects the propagation and evolution of solitary waves on the reef. The segmented submerged breakwater can enhance the synergistic effect of wave reflection and gap diffraction, thereby reducing the maximum wave height transmitted to the reef flat. When the incident wave height is large, the turbulent dissipation effect in the middle area of the segmented submerged breakwater can significantly reduce the transmission wave height, and the maximum wave height increases monotonically with the increase of submergence water depth and incident wave height. The complex flow field near the breakwater dissipates a large amount of wave energy, thereby reducing in the maximum wave height on the backreef slope and achieving the purpose of wave prevention and embankment protection.