The 2004 Aceh tsunami tragedy was one of the most catastrophic occurrences, resulting in damage and severe casualties in multiple countries. This study proposes a hybrid coastal protection system made up of mangroves, a sea dike, a trench, or a combination of the three structures to prevent similar devastation in the future. This system is expected to reduce the tsunami wave height, thus lowering their potential damage. The tsunami wave propagation is reproduced using a nonlinear shallow water equation model. To construct a numerical scheme, a staggered grid finite volume method is implemented. This scheme is then validated using several benchmark tests. Once validated, the computational results are compared to experimental data collected at the Laboratory of Coastal Dynamics in Yogyakarta, Indonesia. Both the physical and numerical models use the downscaled Aceh tsunami waves and real bathymetry. Several scenarios of structures combination are presented with the aim to determine the most effective combination. A sensitivity analysis is also conducted to support the results.