Purpose of this article is to consider methodological and organizational approaches in managing the development of the Arctic zone of the Russian Federation as a complex system at various levels, from the project level to the global level, taking into account the synergy of the potential of the economic platform and the synergy of risks and threats. Methods: the research presented in the article is based on the use of theoretical foundations of managing target processes for solving complex Arctic development problems, applying methods of system analysis, operations research and economic analysis of the development of complex systems from the view of synergy effects. Methods for analyzing the emergence of complex systems, the balance of dynamic integrity, evolutionary development and chaos management, and specific resistance activity were also used. Results: mnsideration of the experience of the complex intensification of the Russian Arctic economic potential at different territorial levels through the system filling with better synergies management of the potential of private-state partnership is presented. It makes possible to identify both the results achieved and the current and future threats and challenges of the region. The author of the study disclosed the organizational and methodological problems of Arctic management, assessed the limitations for the full-scale launch of synergistic management models. Conclusions and Relevance: the presented results of the analysis set the management vector for maximum synergistic activation of financial, logistical and intellectual resources to achieve sustainable, holistic and safe development of the Arctic. The proposed methodological approaches will minimize synergistic resistance of risks and threats to the current policy of the Russian Arctic competitiveness growth.