The construction of artificial island can greatly change the reef hydrodynamics, leading to increased water level and wave height as well as changes in flow field distribution. These alterations can affect sediment transport on the reef, and increase the risk of overtopping and structure instability. A numerical model based on the Reynolds Averaged Navier-Stokes (RANS) equations and k-ε turbulence closure model was developed to investigate the influence of artificial island on reef hydrodynamics. The numerical model was validated against the experimental results of wave height, mean water level, and wave breaking morphology. Detailed flow field, wave height, and wave set-up in front of artificial island were further analyzed based on the validated model. After building the reef-top structure, the wave breaking and offshore currents at reef edge were amplified. The flow stratification and increase of the wave set-up were also found on the reef flat. Furthermore, we found the relationship between maximum flow velocities on the reef flat and incoming wave conditions could be characterized by two non-dimensional parameters: |u¯|max/g(η¯+hr), (η¯+hr)/Hi.