A fundamental requirement for the successful economic development of any modern country is an efficient transport system. Within the framework of an efficient transport system, maritime countries additionally face the complex problem of transport connection between islands and the mainland as well as between islands. The higher the coast indentation index and population density, the more pronounced the problem of the traffic connection between the islands and the mainland. The transport connection of the island with the mainland and between the islands, its influence on the economic development and demographic profile of the island, and the quality of life of the island population is a topic that has been addressed by numerous scientists. However, the field of optimization in maritime passenger transport, with an emphasis on the optimal utilization of the existing resources of the coastal liner maritime passenger transport system, has not been sufficiently researched. This doctoral dissertation gives a contribution to the optimization of maritime passenger transport. The main goal of the research is to create a model for the optimization of the coastal liner maritime passenger transport system. Using the appropriate Edmonds algorithm and graph theory methods, the model determines the optimal arrangement and distribution of ships, from the aspect of fuel consumption and from the aspect of ship availability, i.e., the balance between these two goals, within the existing liner network. In this way, a higher efficiency of the existing transport connection between the island and the mainland and between the islands will be achieved, and conditions for the improvement and long-term sustainability of the coastal liner maritime passenger transport system from an ecological, a social, and an economic point of view will be created. Therefore, the expected scientific contribution of this doctoral dissertation is the systematic analysis of the coastal liner maritime passenger transport system, the analysis of the transport and maritime policies in the European Union, the definition of basic criteria for matching a ship with a shipping line, and the creation and application of a system optimization model with the aim of improving and creating preconditions for the sustainable development of the coastal liner maritime passenger transport system. The developed optimization model for the coastal liner passenger transport system is applicable in maritime transport for entities that create a policy of sustainable transport development, such as the state and shipping companies. The state can use this model in the selection of the optimal ship for a given shipping line, which has an impact on more rational financing of the state shipping lines and further investment in the development of the IV system, while the shippers using this model can use their resources more efficiently to better position themselves in the market.