The need for the qualitative development of integrated transport management systems within transport and logistics systems (TLSs) is due to a number of conditions preventing the efficient movement of goods in Russia and its regions. Planning, organization, and management of freight transportation processes in a transport and logistics system is based on the processing of information about the state of objects in the transport and logistics system by processing statistical data. The development of methods for planning, organizing, and managing terminal and warehouse complexes (TWCs) of transport and logistics systems based on optimizing the interaction of transport and logistics infrastructure facilities creates additional prospects for reducing the costs of freight transportation in Russia and its regions. This approach shall be based on the development of scientific and technical solutions for improving the efficiency of TLSs and TWCs. To implement the process of optimizing freight flows within an intelligent transport system based on digital technologies, it is necessary to develop an appropriate mathematical apparatus adapted to specific tasks. The article provides an approach based on the synthesis of computer modeling methods, which makes it possible to conduct an experimental research program based on an integrated methodology for organizing and managing the interaction of TWCs and transport infrastructure facilities. © 2021 Elsevier B.V. All rights reserved.