A multi-level simulation program developed to compute the ocean current was applied to calculation of storm surge. The program was modified to be able to treat domains of different mesh size for the purpose of simulating phenomenon in the interesting domain in detail as well as setting the open boundary as far as possible. The characteristics of multi-level model in the calculation of wind driven current were demonstrated for the case of a simple rectangular basin. Then, the model was applied to calculation of storm surge in Tokyo Bay. The results were compared with those of two-dimentional model to verify the newly-developed multi-level model program. Sea level and vertically-averaged horizontal velocity obtained by both models agreed well. It indicates that two-dimensional model is usefull for the prediction of sea level or vertically-averaged horizontal velocity. However, the results of simulation by multi-level model showed that current fields of upper and lower levels differed significantly from each other, and also differed from the vertically-averaged current fields. Multi-level model is able to clarify the structure of vertical shear current and the distribution of vertical velocity in the storm surge. In addition, numerical simulations in which the domain around the Port of Tokyo was divided into small meshes were carried out, and the characteristics of the current field were discussed. Furthermore, another simulation was performed to include both effects of storm surge and tide. As the results, it was shown that the sea level might be excessively high under the simultaneous action of storm surge and tide.