Problems of managing hierarchical large-scale transport and economic systems, including producers, carriers and consumers of products, are considered. The task of optimal synthesis of the mechanisms of functioning of large-scale transport and economic systems in conditions of full awareness was set and its solutions were found. On their basis, institutional mechanisms have been developed for the operation of large-scale transport and economic systems, as well as procedures for planning and stimulating their elements aimed at achieving the goal of the large-scale transport and economic system as a whole.