The container transportation and containerization for the material movement has been increasing rapidly in recent years. Under this circumstance, the adequate container terminal with high performance is required to satisfy the needs of customers such as cargo owner and shipping company. The purpose of this paper is to evaluate functional assessment of efficient container terminal and to consider for higher performance of container terminal. First, the process information of container operation is extracted through the database that is constructed by analysis of the daily work report of practical container terminal. And the formulae of skill factor of operator including a driving speed and some troubles of transfer crane is defined, and this skill factor is calculated by comparison of operation time of constructed database and defined the standard for operation time. Finally, a Petri-network model of container handling is proposed for estimation of performance of container throughput.