Abstract: The unique geomorphological structure of coral reef coasts can play a natural buffer role in the waves, thereby effectively reducing the damage of waves to the coast and protecting the safety of the densely populated areas behind. However, the increasing human activities on the reefs, such as coral sand reclamation and infrastructure projects, not only threaten the fragile ecosystems of coral reefs, but also significantly reshape the wave hydrodynamic environment of the reefs, and affect the coastal protection role of the reefs. Currently, reef construction is faced with the dual need of ecological restoration and improvement of the wave-resistant characteristics of the reefs. Based on physical model experiments, this paper systematically studies the changes in hydrodynamic characteristics of regular waves on coral reefs in the presence of ecological artificial reefs, and analyzes the influences of four factors: incident wave height, reef flat water depth, wave period, and reef porosity. Results show that the presence of ecological artificial reefs significantly impacts the propagation and transformation characteristics of regular waves and wave run-ups on the reefs. The interaction between incident waves and artificial reefs is complex, and the presence of ecological artificial reefs can significantly reduce local wave heights near the reef edge and reef flat and decrease wave run-up on the reef flat. Additionally, the complex vortex field inside the ecological artificial reefs dissipates more wave energy, resulting in the reduction in the maximum wave run-up on the slope behind the reef, thereby achieving wave protection for the coast.