Multimodal container terminals are an important part of the logistics systems in international trade. Any improvement in the terminal efficiency is likely to reduce the costs of transporting goods, and to strengthen the trading position of the nation. During the import process, containers flow from ships to the storage yard for temporary storage and then are later moved to the hinterland by rail, or by road. The export process is the reverse of the import process. From the marshalling area, it is possible for a yard machine to carry an inbound container to the storage area and back with an inbound container in one round trip. This thesis investigates the inbound and outbound container process of multimodal container terminals in a multi-ship and multi-berth environment. The aim is to develop mathematical models and analytical tools for yard operation and planning. This study concerns the yardlayout, storage locations, operation strategies as well as the sequencing and scheduling of container process. Several models are developed for the scheduling of container process, taking account of planned and unplanned disruptions, and the intermediate buffer at the marshalling area. The problem is NP-hard and real-life problems often involve large number of containers. In addition, many schedules may not be feasible due to deadlock or violation of precedence-constraints. Good results were achieved on benchmark problems using the proposed innovative. In dealing with unplanned disruptions, reactive scheduling approach was found to give the results similar to as if the disruptions were planned in advance. Numerical investigations are also presented on various factors affecting the efficiency of seaport container terminals including the number of yard machines, and the number of quay crane. As with the various yard-layouts studied, it was found that containers are best stored in rows perpendicular to the quay-line with about 10 to 14 bays in each row. For a shorter ship service time, ideally the containers should be stored as close as possible to the ship. The best storage locations, however, are scarce resources and are not always available. Another model is developed for the best storage location as well as the best schedule for the container process. From an initial best schedule with predefined storage locations, the problem is solved by iterating through the refinement of storage scheme and re-scheduling. At a seaport terminal, ships are planned to arrive and leave within a scheduled time window. Nevertheless, a ship may arrive late due to poor weather conditions or disruptions at the previous port. Such delay may also affect its departure to the subsequent port. To minimise the impact of ship delays, port operators must consider alternate arrangements including re-assignment of berths, re-sequencing of ships and rescheduling of the container process. A ship delay model is developed and the problem is solved by combining branching and Tabu Search. The models developed in this thesis establish the relationship between significant factors and the options for increasing throughput by discovering the bottlenecks. The models are applicable as decision tools for operation planning, yard layout, and cost and benefit analysis for investment in infrastructures.