The article studies the issues of improving the methodology of formation of the innovation development strategy of Russian regions. The hypothesis of the study is that innovations support the territorial growth and may be applied in any territory. However, the implementation of the innovation paradigm at different territories has essential features, which are mostly determined by the industrial and technological type of a region. The author substantiates that successful reindustrialisation and quality improvement of human potential in the Russian Federation demand innovation scenario. I reveal the major problems impeding the innovation activity in Russian regions as well as the consequent threats to socio-economic development in the contemporary network society and globalization. The article shows that in the management of the Russian Federation, the ideology of the industrial period of the mid-20th century has been dominated, when innovations were seen as peripheral in relation to the development of the industrial complex. The author considers the modern theoretical views on innovations as a driver of socio-economic growth as well as the implementation approaches used in international practice management of territorial development. I have revealed the basic trends and features of mutual influence and interaction of innovative and traditional factors of territorial socio-economic development. The author’s methodological approach to grounding the regional innovation system is presented. This approach is based on the mutual consideration of innovative and industrial-technological elements of regional development when choosing the priorities of innovation strategy. The author substantiates the key elements of the innovation strategy for the regional development in relation to the territories of industrial and technological types. The paper presents the calculations assessing the priority for the development the centers of innovation activity of different specialization in the regions of the Russian Federation. The results of the study allow to implement the main principles of the concept of non-price competition when elaborating the strategy of innovation development and choosing the ways for the innovation systems of the Russian regions.