Operation of ship requires a reliable support system of main engine. This paper proposes new models in System Dynamics(SD) simulation for determining the reliability degradation of ship machinery components which are installed in main engine support system. This study purpose is to optimize the availability and minimize the total operation cost which are comprised of running, maintenance, penalty and downtime cost. Reliability analysis is taken into account based on failure rate data record. There are two SD models in this paper. An optimization model endeavors value of minimum Reliability Index(RI) as decision to obtain the highest availability and the lowest total cost. The forecasting model constructs the maintenance judgment when RI reaches the minimum RI in next subsequent voyage. Pumps which are operated in fuel oil, sea water cooling and fresh water cooling system are analyzed. Optimization model results optimum total operation cost and availability, while total operation cost in forecasting model is lower.