The paper analyzes the actual directions of cooperation of logistics systems in the context of globalization of the Eurasian economic area and the development of non-resource exports of the state. The dynamics of cargo traffic export of Russia in the period of 2008-2017 is shown in comparison with the dynamics of cargo traffic import. The authors note that the export potential of the state is related as well to the reduction of import ratio in the inner market. The authors estimated the state of the Russian market of the transportation and logistics services (TLS) taking into account its specifics, carried out the analysis of global trends of the logistics services development. Both the changes in the TLS structure and re-orientation of international cargo transportation of Russia to the markets of Asian countries are observed. The paper pays special attention to the analysis of the strategy of development of the partnership relations in the supply chains in which the potential for the decrease in the cost of the goods and services lie. The authors note that it is possible to develop the technique of optimization of the logistics transportation costs for the countries-members of the integrated process of the Eurasian Economic Union on the base of the innovative logistics concept only which allow simulating the processes within the supply chain in order to align transport processes, specify the competition rules, harmonize the legislation for better use of transit potential and cargo transfer. The study showed the significance of the industry and logistics clusters for the development of the economy of the RF entities and the role of the logistics systems of the state economy entities in their formation on the basis of public-private partnership. The authors determined that the state economy entities should integrate to the international supply chains through the complex implementation of the cluster, logistics approach to the management of multiple supply chains in the regions.