The scientific and technical infrastructural aspects of substantiating the conditions for the deeply integrated development of Siberia, the Far East, and the Arctic zone of Russia are considered. Such development is based on the creation of transport and logistics corridors between Europe and Asia on the basis of the Northern Sea Route, as well as the Trans-Siberian and Baikal-Amur railways. In these corridors should be located multimodal terminal and logistics centers. These centers should be integrated into the transport infrastructure of Siberia, the Far East, and the Arctic zone of Russia. To this end, rail, road, air, and inland water transport links between the Northern Sea Route and the indicated highways should be organized. The conditions for the coordinated development of transport, energy, information, and telecommunications infrastructure of Siberia, the Far East, and the Arctic are defined. A set of tasks for the development of this complex infrastructure is considered. Models and methods have been developed for solving these problems using the apparatus of the theory of large-scale transport systems. They include models and methods for constructing transport corridors, clustering of large-scale networks, integrated assessment, and ranking of complex projects and energy efficiency. The developed models and methods were used to develop plans for the development of the complex infrastructure of Siberia, the Far East, and the Arctic zone of Russia for the period until 2050.