The potential tsunami hazard for atoll islands inside the South China Sea (SCS) has not been investigated previously. In this study, we assess the tsunami hazard for the Xisha Archipelago using a deterministic approach. The tsunami source considered in this study is hypothesized earthquakes in the Manila subduction zone. We employ COMCOT (COrnell Multi-grid Coupled Tsunami model) for tsunami simulations. Different with previous deterministic assessments, our study investigates the uncertainties caused by bathymetric resolution and rupture complexities (here refers to rupture speed and direction variations related to fault geometry complexity). Comparison between results of different resolution suggests that coarser grids may over/underestimate tsunami hazards around mid-ocean atoll islands and this depends on the surrounding bathymetry. But results of different datasets show that GEBCO may lead to a lower result than the multibeam data. We also investigate the uncertainties caused by different rupture speed and direction, which are highly affected by subducting seamounts/ridge. Different rupture direction will shift the hardest hit locations to areas, which are possibly underestimated in cases of instantaneous ruptures. Also, the distribution of slip and location of the rupture zone can affect the local tsunami wave height significantly. We suggest that near-island high-resolution bathymetric data and dynamic rupture process should be considered in future tsunami hazard assessment in locations with similar geological structures.