Existing design codes for coastal defense structures built on coral reefs are scarce compared to those for traditional sandy or muddy beaches. A three-dimensional numerical wave flume is developed to investigate monochromatic wave interaction with a vertical seawall located on the reef flat. The Navier-Stokes equations for two-phase incompressible flow, combining with methods of Large Eddy Simulation (LES) for turbulence closure and Volume of Fluid (VOF) for tracking the free surface, are solved. A set of large-scale laboratory experiments are performed to validate the adopted model in terms of free surface, velocity, dynamic pressure as well as overtopping discharge around the seawall. The model is first applied to examine the cross-shore evolution of waves and flows associated with breaking wave interaction with the seawall. Subsequently, a series of numerical simulations are implemented to study the impacts of different hydrodynamic (incident wave height, incident wave period, and reef-flat wave level) as well as reef and seawall morphological factors (fore-reef slope, seawall position and seawall crest width) on the overtopping discharge over the seawall as well as the cross-shore wave impact force acting on the seawall. Finally, new empirical formulas are proposed, respectively, to predict the overtopping discharge and the wave force.