Complex systems have long been an integral part of contemporary life and can be found everywhere. Modeling, management and optimization of complex systems such as maritime is a particularly important component of the knowledge of inspection staff. For many optimization problems such as optimal techniques, compositions, ship processes, optimization goals in systems are complex relationships with respect to a large number of parameters. Mathematical modeling of a situation or phenomenon is the first step to understand possible solutions and, with adjustments whenever necessary, make predictions concerning the studied subjects that are covered in the final paper. Modeling and simulation, as well as optimization approaches, are required to address the significant complexity, workload and comprehensiveness associated with the development and evaluation of design concepts for offshore vessels. Operational researches are computer models of simulated reality, which are applied in the solution of complex systems, which are the basic research issues of the final thesis. However, modeling complex dynamical systems theoretically requires too many simplifications and therefore the new models may not be valid. The final paper examines the issue of research from a maritime point of view. Special emphasis is given to the application of the network diagram model for transportation optimization. Then, the model of the application of the risk method in shipping was processed. The case study shows that using stochastic soft time windows with stochastic freight demand significantly improved gross profit per day better than trying to arrive on time by varying ship speed or within a non-stochastic shipping context.