This paper mainly deals with the appropriation of ship voyage allocation, using a heuristic regression model, in order to reduce total costs incurred in port, yard and at sea under the specific port condition. Because of different behavior of costs incurred in port, yard and at sea, an effort to minimize these costs by adjusting the number of voyages for three ship classes(50,000, 100,000, and 150,000-ton) should be made. For instance, if the port managers attempt to reduce the sea transport cost by increasing the annual allocated number of ship voyages classed 150,000-ton for economies of scale, they have no choice but to suffer a significant increase in queueing cost due to port congestion. To put it differently, there are trade-off relationships among the costs incurred in port, yard, and at sea. We utilized a computer simulation result to perform a couple of regression analyses in order to figure out the appropriate range of allocated number of voyages of each ship class using a heuristic approach. The detailed analytical results will be shown at the main paper. We also suggested a net present value(NPV) model to make a proper investment decision for an additional berth of 200,000-ton class that alleviates port congestion and reduces transport cost incurred both in port and at sea.