A new concept wave absorber is proposed. It is a net type wave absorber. Its efficiency was reported in another publication. Since it is based on new concept, the traditional wave absorber theory is not applicable. It is modeled by introducing damping terms in linearized free surface boundary conditions in this study. The length and the thickness of the wave absorber are modeled by the length and the coefficient of the damping terms. Series of experiments are carried out to get the data for the coefficients of the damping term. The boundary element method is adopted to solve the system. The predicted wave heights show excellent agreement with those of experiments when the lengths of the incoming waves are within the length of the wave absorber.