A theoretical formulation is performed to investigate the wave reflection and transmission ratios by a submerged multi-layered rubble-mound breakwater. This theory, which is based on the linear boundary integral method, can be extended to the multi-layered breakwater with arbitrary cross section. In the theoretical analysis evanescent mode wave is not considered, since fictitious open boundaries are put on the places far from the structure. Therefore the mathematical presentation may be simpler, and computational time shorter. The validity of obtained numerical results is demonstrated by comparing with ones of impermeable and permeable breakwaters. Comparison shows resonable agreement. On the basis of these verifications this theory is applied to the one and two-layered submerged rubble-mound breakwater with trapezoidal type.