<p>Increasing anthropogenic engineering activities on coral reefs have accelerated changes in their topographic and geomorphic features, such as artificial island construction, which contribute to an uneven reef flat and layout of coastal protection structures. Previous research of coral reef wave hydrodynamics frequently simplified coral reef terrain as a step-like structure, overlooking the effects of uneven reef flats and neglecting the influence of human-engineered structures on wave hydrodynamics at coral reefs. As a necessary supplement, this study analyzed wave hydrodynamic properties of tsunami-like waves over an uneven coral reef with a seawall based on the physical experiments. Hydrodynamic influence of wave height and submergence water depth were analyzed in detail based on physical experiments. To further evaluate the hydrodynamic loads acting on the seawall and investigate the influence of reef-step dimensions on wave hydrodynamics, a series of numerical simulations was conducted. Research findings of present study indicate that tsunami-like waves will undergo complex transforming and breaking at the uneven reef flat. The tsunami-like waves will experience a surging breaker at the outer reef flat and a plunging breaker at the inner reef flat. Moreover, backwash water can be generated at the vertical seawall, resulting in additional wave reflection in addition to that occurring at the forereef slope.</p>