This paper considers the main problems of the interaction of various modes of transport in large transport hubs in the Russian Far East and possible solutions for these problems. The throughput of a transport hub depends on a number of interconnected elements—infrastructure, technology, organization, legal aspects, and information solutions. Insufficient technical equipment, disproportionate development of the infrastructure of interacting transport systems, the lack of unified information and communication technologies, and inconsistencies in the actions of operational personnel lead to excessive downtime of rolling stock on the tracks of the station and on the berths of the seaport. The number of wagons arriving at the address of the Far Eastern ports increases annually, while technical equipment, shunting resources, and handling equipment are limited and require modernization. As a result, the work of the transport hub may be destabilized. Under conditions of limited transport hub infrastructure and an increase in incoming transport, there is an accumulation of wagons on approaches to the transport hub and «abandoned» railway trains are formed. The paper presents the results of simulation modeling of the operation of a railway station and a seaport for processing increasing carloads under conditions of existing technical equipment and downtime wagons under cargo operations. Analysis of the carrying capacity of the railway infrastructure of the Vladivostok, Vanino, and Vostochny (East)–Nakhodka transport hubs was carried out. To minimize the time of vehicles in the transport hub, it is necessary to apply modern organizational and technological measures, to improve customs technologies and create a “dry port” terminal for organizing the work of the transport hub through the “terminal-station-port” system, in which the capacity of the railway component of the transport node is considered together with the “dry port.” The lack of logistic principles for management of the flow of goods in the organization of combined transport requires a modern approach to the organization of efficient operation in the transport hub.