The strategic choice of the innovative vector of Russia’s development predetermines the strengthening of the role of regionally oriented production systems (ROPS) in the context of their consistent integration into the trends of neo-industrial technological concepts “Industry 4.0” and “APK 4.0”, digitalization of the economy, the introduction of innovative solutions of the sixth technological order, the integration of science and production. Currently, only 12% of Russian regions (the leading group) are fully included in the innovation agenda. It is rather difficult to strategize innovative changes within a large country, since the regions are largely differentiated in the context of social and economic development, innovative activity, and the state of scientific and technological potential. The ability of each region to designate its own “window of opportunity” in priority activities, taking into account the imperatives of neo-industrial development, is especially in demand, as it will make innovation processes more manageable. This is especially important in the context of the tightening of sanctions restrictions and the actualization of the request to achieve sustainable technological sovereignty of Russia. The goal of decomposition of the factors of innovative development of ROPS implemented in the study is, in fact, a key preparatory stage for an integrated approach to the subsequent development of regional innovation strategies. The three-level hierarchization of factors and their substantiation by subject areas in the methodological aspect is universal both for local ROPS and for regional control systems. A detailed study of the indicated factors is the starting point for positioning the innovative profile of the ROPS and directly affects the effectiveness of the implementation of innovative scenarios in industries and the agro-industrial complex. The formation of a comprehensive understanding of the innovation situation in the regions contributes to focusing efforts on stimulating the innovation activity of the ROPS, taking into account regional specifics, which fully corresponds to the goal-setting of the Concept of Technological Development of Russia until 2030, which is scheduled to be approved this year. In the next three years, the state will allocate about 4 billion rubles to subsidize innovative technological entrepreneurship. 11 federal development institutions and 46 regional corporations of regional and interregional profile are involved in active support of the innovative development of the ROPS.