To explore the influence of embankment on wave propagation deformation in the island reef system，we use the non-hydrostatic wave model SWASH to verify and compare the three-dimensional island reef model test data，and then build breakwaters with different lengths at different positions above the island reef for wave current simulation. The results show that the wave height in the characteristic section of reef flat does not change obviously with the construction of embankment，but the increase and decrease of water changes obviously with the construction of embankment. The longer the embankment length and the larger the embankment distance，the greater the water increase in front of the embankment and the wider the range of water increase. The wave height and increase/decrease water in the fracture characteristic section change obviously with the embankment construction. The longer the embankment length and the smaller the embankment distance，the smaller the wave height in the section，and the more stable the increase/decrease water. The research results can provide reference for similar reef top engineering constructions.