The impossibility to define the clear and uniform operational guidelines for the implementation of sustainable development policy globally proves the necessity to consider the regional level as the key in terms of developing and implementing modern models of sustainable development, in particular, eco-industrial parks and circular economy projects. It substantiates the need to develop and use the modern innovative methodological approaches to the formation of the relevant regional policy. The circular economy proceeds from the flow-based understanding of the character of the production, distribution, exchange, and consumption of goods in the socioeconomic system and, consequently, the turnover of resources and energy within this system. It determines the need for complex analysis and regulation of material and energy flows. These issues constitute the scope of research of industrial ecology and, at the same time, logistics. This causes the question of the integration of these disciplines within the system of scientific and methodological support of the processes of formation and implementation of the policy of sustainable region's development that is as yet little investigated. The article studies the theoretical and methodological foundations of the industrial ecology and logistics, such as objects, goals, methodological principles and approaches, methods, organizational forms, etc. On this basis the ontological unity of these disciplines is brought to light: they simultaneously study the different, mutually reinforcing aspects of the industrial system's performance through the accentuation of the flow form of the organization of the movement of resources, information, and energy as an object of regulation in such system. The integration of the "environmental" vision of material flows of the regional system, as is characteristic of the industrial ecology, with their "economic" content, which characterizes the structure of the regional economic system and constitutes the object of the logistics studies, should be considered as the basis for the formation and implementation of the policy aimed to achieve the region's sustainable development goals.