In the article the basic aspects of the methodological approach realization in the system of the inverse connection of the fundamental concepts with the three-tier innovative model of the human reintegration in the economic history and theory. The necessity of the further development of the spiritual productive forces of the society, as the basics of the formation of the innovative economics and knowledge economics, is proved. The model of expansion and deeping of the institutional theory on the basis of historical and economical researches of sectoral and intersectoral institutions, and their internal organizational subsystems in the modern TNCs, alliances and clusters, is proposed.