A viscous flow-based computational fluids dynamics model is proposed for the treatment of the water wave and a submerged membrane breakwater interaction.The Navier-Stokes equation is solved using the high-order difference method，and the finite element method is used for the structural dynamics equations.A modified ghost-cell immersion boundary method is used to achieve high-precision coupled solution of fluid and solid solvers.The interface reconstruction is realized by the fluid volume method，and the validity of the model is verified by comparison with the experimental results.Numerical simulation of the interaction between regular wave and a submerged fluid-filled membrane breakwater with different filling degree is carried out to find the appropriate filling degree and explore the wave elimination mechanism.The results show that：1）The numerical model developed can effectively simulate the wave deformation and structural response during the wave passing by the submerged fluid-filled membrane breakwater.2）The large vibration of the inadequate submerged fluid-filled membrane breakwater is more likely to promote the evolution and shedding of vortices near the structure，and is accompanied by the dissipation of energy.