Interaction of waves and a permeable structure is an attractive subject to coastal engineer. In present study, a new concept slit caisson breakwater is proposed, which has embedded channels for fluid resonance in the channel. When the amplified flow is passing through the slit plate, the incident wave energy is dissipated by flow separations. In order to evaluate wave energy dissipation performance of the breakwater, this study has focused on the wave reflection from the breakwater by using numerical simulation and hydraulic model test. The numerical experiment was carried out by Galerkin’s finite element model based on the linear potential theory, and the hydraulic model test was performed in a two-dimensional wave flume at KIOST. Comparison of the numerical results with hydraulic model test results shows proper agreement over wide wave periods. The performance of slit caisson breakwater with the embedded resonant channels was tested with various design of the embedded channel. This breakwater has advantages compared with conventional slit wall caisson breakwater. First, the channel design to control the target wave condition is easy and applicable to long wave periods for dissipating wave energy. Second, this breakwater has structural safety of slit members because the members are not exposed to impact load at near free surface, directly. When the incident wave period and natural period of water column in the channel were matched, the considerable wave energy dissipation was occurred. From this reason, the wave load acting on the breakwater is decreased by wave energy dissipation. The wave reflection characteristics were affected by the porosity of slit plate, the channel width, and the number of channels. Therefore, this breakwater is expected to economical and efficient coastal structures.