Marine transport is a waterway based, extremely competitive means of transport providing transfer of high volume of cargo over long distances in the possible cheapest way. Marine transport system consists of ships, ports, waterways, intermodal connects, supportive systems (e.g. education, finance, customs, insurance etc.), and system users components. As nature of global trade developments, marine transport system components specialise on certain cargo types. Thus, it is possible to differentiate and to categorise marine transport systems for each major cargo types of seaborne trade. Evidently, containers are one of the main cargo types of shipping business at present and around 17% of total seaborne trade volume as weight is carried in container boxes. If we look at the value of cargo carried, we can notice that much higher proportion of seaborne trade as value is carried in container boxes. The marine transport system specialised on container cargo type can be called as “marine container transport system”. From a system science point of view, marine container transport system started systematically “being” to enable “door to door” delivery of various industrial products from shipper to consignee via utilisation of standardised transport units on integrated different means of transport. Characteristically, marine container transport system is a complex system obtaining many adaptive capabilities. Since first container shipped in 1956, container transport has experienced various adaptive changing enforcement from the system environment and achieved significant complex adaptive developments in the dynamic system environment. One of the main objectives of this research is to determine development of system properties and functions of global marine container transport system to have clear comprehending on chronological system development direction stages and underlying self-organisation dynamics of marine container transport system. Furthermore, this research mainly focuses on analysis of actual state of present marine container transport system operations and raising business trends. By the guidance of raising business trends and known significant further system environment changes, this research mainly contribute to forecast adaptive development and self-organisation of marine container transport system for upcoming years. Ship size enlargement trend effect on container shipping, competition of new generation shipping alliances, utilisation of the LNG as a marine fuel for container ships, and effect of new canal extensions and constructions on container shipping are determined as four main adaptation directions for marine container transport system. Operational research network modelling approaches, Cournot oligopoly competition model, cooperative and non-cooperative game theories, system dynamic simulation, and decision making systems are main methodologies of these research. Findings of this research will provide huge benefits to well establishment of future planning strategies and critical decision makings of marine container transport stakeholders.