In order to become a mega hub port, major ports all over the world are making every effort to enhance their productivity through efficiency of internal operation. Accordingly, in order to enhance the competitiveness of a container terminal, an automated container terminal is considered as the best alternative. An automated container terminal is using such automated handling equipment as AGV(Automated Guided Vehicles) and ATC(Automated Transfer Crane). The efficient equipment operation plays a critical role in enhancing the productivity of an automated container terminal. In an automated container terminal, the most important equipments are AGV and ATC. Each block of containers with a vertical layout is generally operating two ATCs. The two ATCs can be crossed or not at each block. In the case of operating crossover ATC, it has an advantage of high flexibility that ATC work is possible at both TP(Transfer Point) of each block. But it has also a disadvantage that the yard has to be operated at a low storage level of containers in the terminal yard. Recently, for automated container terminals, which are being prepared for opening in Korea, they plan to use uncrossed twin ATC in order to make the storage level of their yards high at a low cost. Therefore, studies have to be made in order to increase the efficiency of twin ATC system based on the flexibility that the crossover ATC system has. This research aims to suggest an operation strategy to improve efficiency of twin ATC at each storage block in a yard.