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High winds, ocean current as well as wind-induced ocean waves can affect ship safety and navigation cost. To avoid such rough ocean states and make use of beneficial ocean current, an exact ship position considering about the weather and ocean information is of great importance. In our study, a powerful typhoon in the Kuroshio Current area of the East China Sea was studied to construct the Numerical Navigation System. Information of ocean winds, wind-induced ocean waves as well as the strong western boundary Kuroshio Current is firstly generated by modern weather and ocean models as a combination and then provided to a ship maneuvering model to construct a numerical ship navigation system. Effects of typhoon, wind-induced ocean waves as well as ocean currents on ship navigation could be found quantitatively by utilizing this method.