Wave nonlinearity can drive the near-bed sediment transport and nutrient delivery on coral reefs. Previous studies have primarily concentrated on the wave nonlinearity evolution for a specific cross-shore profile and have scarcely taken the effects of currents into consideration. To better understand the nonlinear wave transformation on reef coasts, the wave height distribution and wave nonlinearity evolution are analyzed based on 3D reef-lagoon-channel experiments in a wave basin. By taking the current velocity into consideration, the Glukhovskiy distribution function is improved in calculating the probability of large wave height in the sequence. Wave skewness and asymmetry on the reef and in the channel are parameterized with the Ursell number considering the Doppler effect induced by opposing or following currents. The accuracies for estimating wave skewness and asymmetry are improved by 39% and 66%, respectively. The influence of Doppler effect on wave shapes on the reef flat and in the channel varies significantly with the incident wave heights and reef submergences. Furthermore, it is also noticed that the reduction of local water depth caused by the propagation of infragravity wave troughs increases short-wave skewness at individual wave scale on the middle of reef flat, while its effect on short-wave asymmetry is not significant.