Recently, there has been an increase in the construction of various types of coastal structures for efficient wave dissipation, seawater exchange, and so on. Among these, a perforated slit caisson has been widely used to reduce the reflected wave energy and the wave pressure on the structure. Therefore, many studies on the wave force on a caisson, as well as the wave reflection from it, have been carried out with laboratory experiments and numerical analyses, considering it as a 2-D problem. However, because a structure like a perforated slit caisson has a variable 3-D shape, waves forces should be considered as a 3-D problem. Therefore, in this paper, a fully-nonlinear 3-D numerical model (LES-WASS-3D) is proposed to examine the reflection characteristics of a perforated slit caisson with two chambers. The numerical model, LES-WASS-3D, was verified in a 3-D wave field by a comparison with existing experimental data for wave reflection coefficients. Then, using the numerical results, the reflection from a perforated slit caisson with two chambers was examined in relation to wave steepness, chamber width, and the shape/porosity of perforated slit.