Wave transmission over a coral reef is very complex，and the wave breaking over the reef flat has signifi-cant impacts on the reefs and the breakwaters． In order to better understand the characteristics of regular waves propagating over the coral reefs，a wave numerical model based on Ｒeynolds-Averaged Navier-Stokes equations was constructed． The turbulence model was designed with two-phase k-ω SST equations． The numerical simulation was carried out in open source library，OpenFOAM． The numerical model was validated with the experiments in the lite-rature． Wave heights，wave setups and surface elevations on the coral reef were analyzed and compared with the results of standard k-ω SST model． The results show that two-phase model can significantly weaken overproduction of turbulence energy near the free surface and provide better predictions of wave height and setup than standard model． Wave breaking in the surf zone causes large turbulence energy at the wave crest while little at the wave trough． Under the effects of turbulence energy，the wave height decreases and the wave setdown increases at the
breaking point，and the energy dissipation increases after the wave breaking． This numerical model can be used for calculating wave breaking in the design of harbor construction．