The article explains the development of simulation models’ structure of intermodal processes using IDEF-models, which takes into consideration the properties of transport junction structure handling export shipment operations. This procedure is necessary for notifying the distribution laws of transport flow at transport junctions when economical affairs between market subjects have been changed. Method of choosing the simulation tools has been offered based on hierarchy analysis method basis, which follows the specifications of modeling of intermodal transport at transport junction. The usage of optimization algorithm for freight flow delivery by railway to seaport stations is able to reduce wagons’ downtime. The effectiveness of produced algorithm of automatization has been explored and founded out that algorithm of multiagent optimization gets the maximum effect in case when sea ports work without interruptions.