A numerical radiative transfer model based on matrix-operator theory to simulate the underwater inelastic scattering is presented. The assumption that various radiant energies decrease approximately exponentially with depth in a homogeneous layer is introduced to incorporate the inelastic scattering process as a source operator to the model. Validation by the Mobley standard problem 7 of underwater radiative transfer and comparison with the results of Hydrolight 5.0 show that the processing of the multi-scattering and inelastic scattering in this model is correct. So we conclude that this model is a suitable tool for simulating all radiative transfer processes under water. Simultaneously, with three-component model, this underwater radiative transfer model is used to simulate the effect of each components of natural water on inelastic scattering and inelastic fraction in the remote-sensing reflectance. The investigation reveals that only in clear water bodies, the inelastic fraction resulted by the water Raman scattering is high. With the increasing concentration of gelbstoff and chlorophyll, the inelastic fraction increases in the relevant wavelength, but either gelbstoff or chlorophyll restrains the inelastic scattering process of each other. And suspended sediments reduce the effect of inelastic scattering significantly which is even neglected in some water with high concentration of suspended sediment.