In the South China Sea, although land reclamation projects on some coral reefs have been completed, these reefs located in far seas are extremely vulnerable to marine natural disasters such as tsunamis and storm surges due to their special marine geographical environment. Given that the protection capabilities carried by the reefs themselves have limitations in dealing with these disasters and cannot fully ensure the safety of personnel and facilities on the islands, it is particularly necessary to construct coastal protection measures near the reefs. Based on wave flume experiments, this paper conducts research on the propagation and evolution characteristics of reef waves and the impact on wave run-up under the action of infragravity waves by submerged breakwaters, and deeply discusses the impact of submerged breakwaters on three aspects of hydrodynamic characteristics, average water level, and wave run-up on the reefs. The research results show that the submerged breakwater significantly changes the hydrodynamic characteristics of infragravity waves, promotes wave breaking in advance, and then causes an increase in the amplitude of infragravity waves in the reef flat area. In addition, in the case of changes in effective wave height and spectral peak period, the submerged breakwater has a significant impact on the average water level of the reef flat and can increase the average water level. However, as the water depth of the reef flat increases and the position of the submerged breakwater moves forward, the average water level of the reef flat shows a downward trend. Further observation reveals that the existence of the submerged breakwater does not have a significant contribution to the contribution of long-wave run-up in changing wave run-up. Whether the submerged breakwater exists or not, infragravity waves play a major role in wave run-up. However, as the relative position of the submerged breakwater decreases and the water depth of the reef flat increases, the contribution of long-wave run-up to run-up will decrease and transform into sea-swell wave run-up playing a dominant role.