Abstract: Coral reefs widely distributed in tropical and subtropical waters generally have uneven reef flat terrain. The change of reef flat terrain will significantly affect the propagation and evolution characteristics of incident waves on islands and reefs. However, previous studies have not systematically studied the influence of reef flat topography mutation on the hydrodynamic characteristics of regular wave island reefs. In this paper, the hydrodynamic characteristics and nonlinear characteristics of regular waves on uneven islands and reefs are studied by carrying out wave flume experiments. The effects of three different incident wave factors, i.e., incident wave height, wave period and reef water depth, on wave propagation deformation and water increase are systematically analyzed. The results show that the non-flat reef flat enhances the nonlinear variation of waves, and the asymmetry, skewness and Essel number reach the peak near the reef flat step, which promotes the transfer of wave energy from the dominant frequency wave to the higher harmonics. The energy dissipated by wave breaking on the second reef flat mainly comes from the main frequency wave, and the second harmonic in the transmitted wave component near the shoreline is equivalent to the energy of the main frequency wave. In addition, the higher the incident wave height or the smaller the water depth of the reef flat, the higher harmonics are more likely to be generated near the reef flat step, and the wave added value on the second reef flat increases. When the wave period is increased, the standing wave will be formed on the first reef flat under the action of multiple wave reflection, and more wave energy will be transferred to higher harmonics near the reef flat step, and the wave increment value on the second reef flat shows a nonlinear change.