The relevance of the topic announced in the title of the article, due to the fact that the modern theory of national security does not fully take into account the current processes of innovative development, does not give answer how to maintain sustained economic growth and sustainable development in the process of formation of innovative economy.  In this article the results of own research, the author has developed a methodologically-theoretical foundations and practical approaches to the provision and operation of a new kind of safety in the period of innovative development, innovative security, which is an integral part of national security. The algorithm of formation of System of innovative security in the conditions of formation of innovative development, which, in fact, is one of the elements of the national Strategy of innovative development. It is concluded that the system ensure security innovation, the formation of the innovation economy, having a relative autonomy, must work in tandem with the system of national security and with the state as a whole.