Abstract: Coral reefs that are widely distributed in tropical and subtropical waters usually have uneven reef flat terrain. The topography of the reef flat terrain may significantly affect the propagation and evolution characteristics of incident waves on reefs. However, the related research work is barely reported. In this paper, a high-resolution numerical wave flume is constructed based on the smoothed particle hydrodynamics (SPH) method. A series of numerical calculations are carried out for the influence of uneven reef flat topography on the hydrodynamic characteristics of tsunami-like waves over fringing reefs. The effects of incident wave height, reef flat water depth, reef flat topography change position, reef flat topography change height, and reef edge slope are systematically analyzed. The numerical results show that the SPH method can accurately simulate the propagation and evolution of tsunami-like waves over the uneven reef flat terrain, and the increase in elevation of the reef flat terrain will significantly enhance the reflection intensity of the incident waves. With the increase of incident wave height, the reflection coefficient also increases gradually. The increase of reef flat water depth may gradually reduce the breaking strength of incident waves, weaken the effect of bottom friction, and gradually increase the wave height and transmission coefficient along the way. The location and magnitude of the increase in elevation of the reef flat terrain will significantly affect the location and intensity of the incident waves. However, the change of reef margin slope has no significant effect on the propagation and evolution characteristics of tsunami-like waves under the condition of uneven reef flat topography.