Keeping in mind the significant dependence of the Russian economy on oil and gas revenues coupled with the low energy efficiency and technology backwardness, the country faces noticeable threats to its technological and economic sustainable development. Findings of a system analysis of the Russian energy sector indicate the need for organizational and technological changes. It is found that easily available opportunities to get raw material rent, along with respective rules of the game, reduce economic agents’ interest to innovations. External risks, such as sanctions, volatile energy markets, are not the root cause of the crisis in Russia, but these factors do destabilize the situation and make modernization more difficult. In this context, strategies and mechanisms that meet internal and external challenges are required. The novelty of the approach is that the improved systemic economic paradigm of innovation strategy formulation and support mechanisms implies moving the development drivers from the category of external impacts on the country’s energy sector to the category of internal imperatives of its technological development through creation and stimulation of innovation and industrial ecosystems where the energy sector will serve as an infrastructure framework that consolidates all sectors of the economy.