To improve our current understanding of tsunami-like solitary waves interacting with sandy beach, a nonlinear three-dimensional numerical model based on the computational fluid dynamics (CFD) tool OpenFOAM® is first self-developed to better describe the wave propagation, sediment transport, and the morphological responses of seabed during wave runup and drawdown. The finite volume method (FVM) is employed to discretize the governing equations of Navier–Stokes equations, combining with an improved volume of fluid (VOF) method to track the free surface and a k–ε model to resolve the turbulence. The computational capability of the hydrodynamics and the sediment transport module is well calibrated by laboratory data from different published references. The results verify that the present numerical model can satisfactorily reproduce the flow characteristics, and sediment transport processes under a tsunami-like solitary wave. The water-sediment transport module is then applied to investigate the effects of prominent factors, such as wave height, water depth, and beach slope, in affecting the beach profile change. Finally, a dimensionless empirical equation is proposed to describe the transport volume of onshore sediment based on simulation results, and some proper parameters are recommended through the regression. The results can be significantly helpful to evaluate the process of transported sediment by a tsunami event.