Sea transport cost is one of prominent components in terms of macro and micro economy. It has also a huge impact on global economic growth and business competitiveness. Many researchers have been involving to define new methods in order to gain the productivity and efficiency of marine transportation system. However, several researches merely focus on local optimum solution, short-term orientation and incomprehensive integration of strategic variables and operational aspects. Therefore, in order to accommodate those criteria into a new system, we should take into account all factors which influence on the whole of marine transportation system. Theory of Constraint (TOC) is a multi-faceted methodology that views the system as a series of processes or events that are interconnected. Even though it has been widely used in manufacturing sector, the application of TOC in the marine transportation system is still limited. This research aims to implement the concept of TOC to develop new tools and methods to resolve the issue of marine transportation as well as to formulate a good strategy at the level of strategic, operational and tactical in order to improve the performance of marine transportation system. The study is conducted at PT.X as one of the providers of sea transport services. Three scenarios are applied to analyse the changing of performance for each constraint when the capacity constraint will be increased by 50, 100 and 150%, respectively. As a result of the Investment Efficiency Ratio, the greatest impact derived from investment activities was obtained from elevation constraint of jetty, the second largest ratios is the elevation constraint of onshore pump capacity and the last is port draft constraint.