The article reveals the theoretical and methodological provisions for the formation of the composition of technological elements of the strategic planning system, their interaction with the resource components of the organization of higher education (on the example of Voronezh and St.Petersburg universities) to achieve generalizing and specific targets of quantitative and qualitative nature of the strategic the goal of long-term development of a higher education institution. The concepts of “strategy”, “strategic vision”, “mission of the organization of higher education” are defined. The possibility of optimizing resource consumption in the process of implementing complex measures within the framework of federal, regional, sectoral and local programs and projects of social, economic and innovative development of higher education organizations is substantiated. The priority directions in the development strategy of the analyzed universities are highlighted. The necessity of including such technological elements as strategic analysis, mission, strategic vision, strategic goal, generalizing (basic) strategy, functional (private) strategies in the system of strategic planning of socio-economic and innovative development of the studied universities is substantiated.