Activation of the processes on globalization and national economic space regionalization actualizes the problem of formation of an effective mechanism for managing the regional socio-economic system, the availability of which ensures effective use of available resources, creates prerequisites for the formation and implementation of the competitive potential of a territorial entity, and is a necessary prerequisite for neutralizing the consequences of global and local crises. The level of sustainable functioning of regional socio-economic systems is a key factor affecting the socioeconomic development of the Russian economy in the face of increasing uncertainty in the external environment. This requires new approaches to identify tools for new governmental management at the meso level, to developing new forms and models for sustainable socio-economic development of regions. The paper substantiates the thesis that the necessary condition for the implementation of sustainable development of the regional economic system is the presence of adapters in its elements that provide a certain quality of management decisions. Regional development is aimed at achieving a set of parameters that meet the needs of economic agents: residents and non-residents of the regional economy, subject to feasibility of management decision, compliance with strategic guidelines for regional development and reducing agency costs. At the same time, regional development is interpreted as the result of structural changes (the synthesis of structure and processes) in the system of interaction between subjects of socioeconomic relations at the meso level, and controlling is considered as a tool for effective management of innovation changes