Suggestions for the development of theoretical and methodological foundations of system management of energy efficiency and environmental pollution by road transport in the life cycle are given. It takes into account all essential areas covering transportation, infrastructure, maintenance, also energy, chemical and automotive industries, raw material extraction, utilization, and related processes of energy consumption and environmental pollution, distributed in space and time. A universal structural scheme of the “supersystem” is proposed, which reflects the processes of consumption of energy, material and other resources, distributed environmental pollution through the functioning of road transport and related industries, and linked damage as well. The target function of the “supersystem” can be represented as the fulfilment during a certain period (covering the life cycle of the main elements – objects of influence (regulation) and investment of financial resources) of the specified volumes of certain types of transport work with the minimum possible and economically justified consumption of energy, consumables, materials, other resources (including those consumed by the transportation, infrastructure, maintenance, also energy, chemical and automotive industries, raw material extraction, utilization), the minimum possible losses due to artificial pressure on the recipients (human beings, fauna and flora, buildings, etc.) of directly the transport system and infrastructure, as well as side effects of processes in other elements of the “supersystem”, that may be reduced to the total cost of transport, taking into account the inflation index of monetary units. It is proposed to carry out a mathematical description of complicated sets, dynamically distributed in the space of objects that change the structure and properties over time, based on the further development of such a tool as the theory of multisets. In a simplified form, it is presented an example of a fragment of the management system based on measures to regulate the first access of vehicles to the market, further operation, and to certain elements of infrastructure, with the introduction of low emission zones in cities. The development, creation and effective functioning of the management system of transport and related sectors of the economy in those mentioned above and other parts, requires a coherent system approach based on forecasting (modelling) the consequences of decisions, which can be implemented using the tools described in this article. Keywords: wheeled vehicles, road transport, systems management, energy efficiency, environmental pollution.