The dataset contains numerical hydrodynamic model data generated using the XBeach 2DH Surfbeat model for Dongsha Atoll, South China Sea. Three directional numerical experiments are included, corresponding to incident wave forcing from west (W), west-southwest (WSW), and southwest (SW). The archived model data include water-surface elevation (zs), wave height (H), and depth-averaged horizontal velocity components (u and v). These outputs are provided to support the analysis and reproducibility of the associated study of wave transformation and low-frequency wave dynamics within the Dongsha reef–island system. Data for each wave-direction case are stored separately, and a README file provides information on the organization and interpretation of the archived files.