The paper discusses the problem of common transport system creation from system-wide positions. Much attention is focused on two aspects – active self-maintenance in the environment with disorganization and dual nature of an organized object – as a system and as an element of a super-system. These roles for transport are expressed in the presence of two main tasks, for the system it is «transportation», for the element of the national economy – «ensuring economic cooperation by reliable and efficient transport links». In the first case, losses in the interaction of transport and production are attributed to production, in the second – to transport. Therefore, in the latter case, transport has to adapt to the rhythms of production. Self-maintenance on transport is provided by adaptive, flexible, controlled operation. Controlling creates so-called dynamic reserves that replace the actual, static reserves. To organize the common transport system in a market economy conditions it is necessary to use «system integrators». Functions of the «system integrators» should be performed by forwarding companies. Methods of calculation and optimization should represent system properties of transport objects. For optimal control of traffic volume the paper proposes to use a dynamic transportation problem and a dynamic coordination method instead of a transport linear programming problem. The latter allows calculating not only the optimal modes of transportation, but also the adaptive coordination of production and consumption rhythms. These methods have been successfully applied in the empty car traffic volume control and in the calculation of the coordinated supply of goods to seaports. Simulation modeling is considered as the main method of calculation. Authors present two simulation systems: ISTRA for modeling railway stations and IMETRA for modeling transport junctions and large ranges. They have built-in mechanisms for representing the adaptive control. The optimization methods and modeling systems have passed state registration.