A two-layer model, with the upper layer being the perfect fluid and the lower layer being the pseudo-plastic fluid describing water wave attenuation over mud bed, was established. A simplified method based on the principle of equivalent work was applied to solve the boundary value problems. The computational results of the model show that the two-layer perfect fluid model and the perfect-viscous fluid model are all special cases of the present model. The complex nonlinear properties of wave attenuation over mud bed, can be explained by the present model, e.g., the wave dissipation rate decreases with the wave height in certain cases, while the small wave propagates over mud bed with less energy dissipation and large wave attenuates rapidly in other cases. Other factors influencing the wave attenuation were also discussed.