Based on the nonhydrostatic single-phase flow numerical wave model (NHWAVE), the propagation of random waves on a permeable fringing reef is simulated numerically, and the effects of incident wave height, water depth on reef flat, spectrum peak period, thickness of permeable layer, porosity and median diameters the hydrodynamic characteristics of waves on the fringing reef are considered comprehensively, focusing on the variation of sea-swell wave height, infragravity wave height and mean water level along the reef, and comparing with that of the fringing reef without permeable layer. The study shows that the existence of the permeable layer has a significant impact on the hydrodynamic characteristics of waves on the fringing reef. The study shows that the existence of the permeable layer reduces the shallow water deformation of waves on the slope in front of the reef and the wave breaking near the reef edge, and significantly decreases the sea-swell wave height, infragravity wave height, and wave setup near the shoreline, in addition to that, the existence of the permeable layer reduces the maximum wave runup on the shoreline. The greater the incident wave height and spectrum peak period, the more significant the effect of the permeable layer on the sea-swell wave, infragravity wave and wave setup on the fringing reef; when the water depth of the reef is increased, the effect of the permeable layer on wave attenuation is weakened; as the thickness of the permeable layer increases, the values of sea-swell wave height, infragravity wave height and wave setup near the shoreline decrease.