Nowadays as economies rapidly have developed, the scale of trade and quantities of shipping goods have caused ship size to expand to size never previously seen. In order to being fully effective on employing mega-containerships, at a terminal where mega-containerships are calling, most cargoes to be handled are transshipments from origin to destination ports via that terminal. Thus, associated handling operations are undertaken between mega-containerships and feeder ships. In order to decrease the turnaround time of ships calling at this terminal, smooth handling of operations is of major importance. Normally, the handling time spent for a ship is determined by the number of containers handled and the QC assigned to that ship. However, we consider the above scheduling problems at the terminal with long quay consisted of multiple-berth ranged in a line. Thus we consider the model to estimate the handling time spent for the ship. Additionally, this paper also considers the storage arrangement for transshipment containers which are unloaded from ships (as inbound) and are loaded to other ships (as outbound). Using the estimated time of ship handling, we develop the approach that optimizes the yard arrangement is applied in the genetic algorithm.