Tsunamis induced by megathrust in the Manila subduction zone impose alarming threats to the coastal cities in the northern South China Sea (SCS), and risk assessment of tsunami hazards in this region becomes demanding. One distinguishable geographic feature in this region is Dongsha Atoll, which is situated between the tsunami source zone and the China coastline. This study discusses the role of the Dongsha Atoll in modifying the tsunami impacts through numerical simulations of a group of synthetic tsunami events with [Formula: see text]. Three types of representations for the Atoll in the numerical simulations are employed, specifically (i) the real topo-bathymetry of the Atoll is fully resolved (Model-1), (ii) the Atoll is removed (Model-2), and (iii) the Atoll is artificially represented by a cylinder (Model-3). The results show that without the Dongsha Atoll presence (Model-2), the tsunamis can induce a substantial increment of water level behind the Atoll and in the vicinity of the Pearl River Delta (PRD) region in China. While the results obtained by realistically modeling the Atoll (Model-1) show that a large amount of tsunami wave energy/momentum can be entrapped by the lagoon and slowly radiated to the ocean. The interactions between the tsunamis and the Atoll will lead to severe flooding on the Dongsha Island on the west bank of the Atoll. However, the peak water levels behind the Atoll and at the selected mainland coastal sites are reduced, indicating that the Dongsha Atoll can offer some degree of protection for the region in its behind. Meanwhile, a slightly smaller reduction of tsunami heights is reported in the simulations with the Atoll being represented by a cylinder (Model-3), implying that the reduction effects are sensitive to the representations of the Atoll. Therefore, the full model of the topo-bathymetry of the Dongsha Atoll is recommended for future tsunami risk assessments for both Dongsha Atoll and the mainland in the SCS region.