A new method to estimate and evaluate ship performance in actual seas is investigated from the viewpoint of long term estimation including time depending influence such as fouling and aging effects of hull, propeller and main engine as well as resistance increase due to waves and winds and so on. In order to verify the present method, simulation is carried out. The result shows that the present method gives better estimation for the ship performance such as increase of sea margin, decrease of ship speed and change of the revolution number of propeller, compared with the previous work. The present method should be useful for ship designers to design a ship hull, a propeller and to choose a suitable main engine at the initial design stage under the condition of the deadweight, ship speed and sea condition given by a charter party.