Since the middle of 1950's, containerization has been rapidly spread over the world in virtue of great merits providing to interensts, and the fundamental changes in port management and prot operations are resulted. As the container terminal is a complex system which is consisted of various subsystems, the treatment for improving the productivity is required in a comprehensive fashion, both in each of its parts and as an integrated system. This paper aims to make an intensive analysis of the Busan Container Terminal system, especially focusing on its subsystems such as ship operation system, storage system and transfer system. First of all, the intrinsic capacity of various subsystems is calculated and it is checked whether the current operation is being performed effectively through the formal analysis. Secondly, the suggestion is presented to improve the operation by considering the throughput that the port of Busan will have to accept in the near future. The results are as follows; 1) As the inefficiency is due to the imbalance between various subsystems at Busan terminal, transfer equipment level must be up to 31% for straddle carrier and 67% transfer crane above all. 2) The yard capacity must be increased by reducing the free dwell time of containers in order to accept the traffic volume smoothly in the near future. 3) The better way to reduce the port congestion is to change berthing rule from the FIFP to the Pre-allocated system by considering the ship arrival pattern.