A three-dimensional coupled fluid-structure-sediment interaction model (FSSM) is developed in this study. FSSM consists of an extended Navier-Stokes solver (XNS) with a volume of fluid module (VOF) for air-water interface tracking, an immersed boundary module (IBM) for structure motion tracking, and a sediment transport module (STM) for sediment surface tracking and suspended sediment tracking. In FSSM, a two-way coupling procedure is implemented in each time step to connect XNS with VOF, IBM, and STM. FSSM is applied to wave-induced local scour around a submerged movable short cylinder and resulting burial of the cylinder. The computational capability of FSSM is demonstrated against experimental data in terms of seabed change around the cylinder.