Current market conditions, as well as the reorientation of the Russian economy from raw materials to innovative model of development, based, in particular, on strengthening the position of national industry, able to compete with international level producers, are incentives to seek ways to increase efficiency and develop additional competitive advantages, which in the present are innovative products and services. One of such ways is the integration of economic entities, in particular the formation of integrated industrial structures (IIS). In the article the author shows that the formation of IIS is one of the current trends of economic transformations in the Russian economy. Thus, in the period from 2011 to 2015, the share of transactions in the industrial sector were averaged 31%. The most active sectors were oil & gas, metals & mining. One of the factors of innovative development of economic subjects is the formation and effective use of their innovative potential. The estimation of innovative potential plays an important role for the development of innovation policy and innovation strategy of subjects’ activity of the market. However, the estimation of innovative potential does not allow to comprehensively cover all aspects related to its formation, development and implementation. In the article the author shows that organizational-economic management mechanism of innovative potential of IIS is a system of influencing tools and processes that are used in practice to obtain innovative results. Implementation of organizational-economic management mechanism of innovation potential of IIS allows the structure as fully as possible to adapt to the fierce competition to their market, develop existing technologies and to start new, to produce complex and innovative products by maximizing the use of existing innovative potential and its increase, which finally increases the competitiveness of the structure.