The paper proves that successful innovation-oriented development of the industrial complex of the region can be ensured through the creation of adequate institutional structure. As a theoretical and conceptual platform for this task the use of regional institutionalism is suggested. It is reasoned that integration component plays an important role in providing of the innovative development of the industry in modern economic realities and the potential effects of integration on meso- and micro-levels of economy are provided. Integration of industrial structures potential at the same time assumes expansion of a partner segment of the entities relations in the market environment on the basis of network, cluster, and integration approaches convergence to management in the industrial development. On the basis of the international experience analysis it is illustrated that forming of multichannel partnership of actors in the industrial sphere with a vector on an innovatization requires creation of the corresponding institutional conditions. It is established that the main objectives of the relevant institutes consist in legitimization of various forms and technologies of partnership and stimulation of economic entities interactions. The first problem is solved by means of legal support of integration and partners’ interactions, the second one - with the use of a program and project approach. The basic structural elements and functional areas of regional institutional structure in the context of innovative industry development are determined. It is shown that the institutions of the partnership and monitoring of the obligations implementation by integration formations participants can have formal and informal nature, at the same time the trust institution is especially important. In work significant influence of regional specifics on institutional structure and integration of economic entities is proved.