At present, BEM and VOF methods are two kinds of effective methods for simulating the nearshore wave deformation. A new numerical wave coupling model based on both BEM and VOF methods is established by considering the advantages of both methods. In this model, wave propagation in front of structures is calculated by BEM, and the interactions between waves and structures are calculated by VOF method. The applicability and accuracy of this model are examined by comparing numerical results with the experiment results of wave propagation and deformation around a submerged breakwater. The results show that the present model can accurately illustrate the interactions between waves with structures.