The design of coastal protection structures requires critical design variables such as overtopping rate and wave run-up height. However, conventional design methods, developed primarily for sandy coasts, may not effectively account for wave deformation over reefs. The presence of a reef introduces additional parameters, making simple empirical approaches less effective. This study aims to establish an integrated design method by combining the SWAN model and a Boussinesq-type model, enabling a comprehensive simulation of wave processes from offshore to the reef and structures on the shore. The Boussinesq-type model accurately simulates wave deformation and run-up over reef coasts, showing high agreement with observations. Overtopping rates at a vertical wall were evaluated using both the Boussinesq-type model and CADMAS-SURF, with consistent results across methods. While the Boussinesq-type model effectively captures run-up, it has limitations in reproducing overtopping rates. Therefore, combined use with CADMAS-SURF is recommended. Clearly defining each model’s scope and limitations and using them complementarily enhances the accuracy and reliability of coastal structure design over complex reef coasts.