Most of coastal structures have been built in the surf zone to protect coastal areas. The transformation of waves in the surf zone, in general, is very complicated and contains lots of hazards to coastal communities. Thus, behaviors of waves in the surf zone should be very carefully analyzed and predicted. Furthermore, an accurate analysis of deformed waves around coastal structures is directly related to construction of economic and safe coastal structures because a wave height plays an important role in determination of weight and shape of a levee body or an armoring material. In this study, a numerical model using a large eddy simulation is employed to predict runup heights of nonlinear waves passed a submerged structure in the surf zone. Reduced runup heights are predicted and the characteristics of runup heights in terms of wave reflection, transmission and dissipation coefficients are investigated.