With global climate change and sea level rise, low-lying atoll islands fringed by coral reefs are especially vulnerable to wave-driven inundation during extreme wave events. In recent years, China has implemented large-scale engineering constructions on some low-lying reef atolls in the South China Sea. Hence, accurate prediction of the nearshore waves on the reefs is important to assess the wave runup on such constructed coastal structures. Wave runup near the reef coast is primarily contributed from sea and swell waves (0.04-0.4 Hz), infragravity waves (0.001-0.04 Hz) and wave setup. A typical coral reef profile is characterized by a seaward sloping fore-reef and an inshore shallow reef flat extending towards the coastline, and the reefs have been reported as efficient buffers to the wind-driven wave energy over decades. Reefs often have fully developed coral communities on the fore reef and reef flat, resulting in complex topography and reef surface roughness. The wave energy loss caused by bottom friction maybe even be greater than that caused by wave breaking. This laboratory study modeled a variety of rough surfaces around the reef surfzone by using an array of cylinders with different arrangements. The results show that the swell waves height near the coastline is significantly lower than the incident waves height due to the breaking of the short waves at the reef edge and the continuous attenuation of the friction along the reef flat during the irregular waves propagation to the shore. The infragravity waves height increases significantly at the reef edge due to wave breaking, and then the infragravity waves height are amplified by the resonance effect on the reef flat, and the infragravity waves height increases gradually along the reef until it reaches the maximum value near the coastline. Near the coastline, both the swell waves height and the infragravity waves height increase with the incident waves height and period increasing. The swell waves height increases with reef-flat still water level increasing, while the low frequency long wave height decreases with the increase of reef-flat still water level. Both wave heights with the rough reef surface are found to be smaller than those with the smooth surface. When the roughness of reef surface varies, both wave heights near the shoreline decrease with the increasing surface roughness density. We also analyze the coherence and transfer functions to show that the infragravity waves on the reef flat are generated by the breaker-point shift when the grouped short waves break around the reef edge. Resonant modes exist assciated with the infragravity wave motions on the reef flat. For the smooth reef surface, the infragravity wave energy is amplified due to the first-order resonance when it propagates from the reef edge to the shoreline. For the rough reef surface, the infragravity wave energy is dissipated by bottom friction on the reef flat, and the effect of resonance is insignificant.