Summary: A two-phase flow model has been developed to study three-dimensional breaking waves over complex topography, including the wave pre-breaking, overturning and post-breaking processes. The large-eddy simulation approach has been adopted in this study, where the model is based on the filtered Navier–Stokes equations with the Smagorinsky sub-grid model being used for the unresolved scales of turbulence. The governing equations have been discretized using the finite volume method, with the PISO algorithm being employed for the pressure–velocity coupling. The air–water interface has been captured using a volume of fluid method and the partial cell treatment has been implemented to deal with complex topography in the Cartesian grid. The model is first validated against available analytical solutions and experimental data for solitary wave propagation over constant water depth and three-dimensional breaking waves over a plane slope, respectively. Furthermore, the model is used to study three-dimensional overturning waves over three different bed topographies, with three-dimensional wave profiles and surface velocities being presented and discussed. The overturning jet, air entrainment and splash-up during wave breaking have been captured by the two-phase flow model, which demonstrates the capability of the model to simulate free surface flow and wave breaking problems over complex topography.