Abstract: This article is dedicated to designing of the transport and logistics systems with built-in resistance to structural failures. The sustainability indicators reflect the impact of the failure of one or several hubs (communication channels) upon working capacity of the already functioning system. In the process of designing the system, the sustainability indicators also provide opportunities for optimizing its structure from the perspective of set reliability expectations. The authors give attention to the modeling of the transportation and logistics system on the basis of theoretical-graph toolset, as well as propose sustainability indicators and articulation of optimization task. The structure of transportation and logistics system is described using the instruments of graph theory, definition of the task is presented using the criteria of optimization theory, and limitations are the feasible solutions on graphs are established in the matrix form. The authors suggest a theoretical-graph description of the structure of the transportation and logistics systems, propose multiobjective goal setting, and introduce the concept of structural stability based on the indexes and their threshold values. Proposal is made on the approach towards designing the transport and logistics systems with set parameters of structural stability and tried it on test data.