As a mitigation measure against a tsunami inundation, vegetation-embankment hybrid structures received attention after the 2011 Great East Japan Tsunami, and some structures have already been constructed or are under construction in Japan. The present study conducted a series of numerical simulations using a hybrid system comprised of an artificial structure (an embankment, moat) and a natural component (vegetation) that was experimentally proposed in previous studies as an effective structure for tsunami mitigation. After validating the numerical model using published data, this study investigated differences in the performance of the hybrid system by changing the tsunami period and height characteristics of the tsunami-like surge-type flow. As a result, the delay in tsunami arrival time (ΔT) was not affected by the tsunami wave period for the investigated hybrid structures. Among the investigated structures, Case Ve40ME (where Ve40, M, and E represent vegetation, moat, and embankment, respectively, in that order from seaward) showed the maximum performance of ΔT. The reductions of overflow volume (ΔQ), fluid force index (RFI), and moment index (RMI) declined during the tsunami period. The tsunami mitigation effect is closely related to the relationship between the development times of backwater rise, hydraulic jump, and the tsunami period. Case Ve40ME was effective for ΔT, ΔQ, and RMI. Case EMVe40 was especially effective for RFI. When the tsunami period is short, the water level at the shoreline starts to decrease before full development of the hydraulic jump generated in the hybrid system. Thus, overflow volume to landward decreases, and the mitigation effects increase. When the tsunami period is long, the receding phenomenon at the peak water level does not affect the maximum values, thus the mitigation effects become smaller compared with the short period. However, the superiority to other structures is maintained in Case Ve40ME and Case EMVe40 with seaward vegetation and landward vegetation, respectively.