Ocean environment attracts more and more attention, whereas monitoring ocean environment using ocean color imagery (e.g., MODIS) has become one of the important fields in modern oceanography. After analyzing a few individual modules of the radiative transfer process, an end-to-end numerical model for ocean remote sensing is developed. This model combines MODTRAN and HYDROLIGHT, both are state-of-the-art radiative transfer models for atmosphere and water, respectively. Also, a simple but realistic cloud model is added to it. This combined model calculates the downward radiance on water surface using MODTRAN and the independent cloud model, which replaces the empirical and semi-empirical models used in RADTRAN (Gregg and Carder 1991). Especially, with information of cloud's location and brightness from by the cloud model, the combined model provides more accurate radiance on water surface. Further, the effects of cloud position (from 30 degree to 180 degree for the cloud central azimuth angle) and coverage (from about 10% to 80%) on retrieved chlorophyll concentration by standard MODIS algorithm is analyzed. It is found that the nearer the cloud to the Sun the smaller the effect on the derived chlorophyll.