The article is devoted to some methodological features of modernization in modern education in the context of "the knowledge economy" development which is aimed at shaping new mental potential of the modern state. Features and prerequisites for the emergence of the knowledge economy, the priorities of which include the development and spread of information technologies, development and introduction of innovations, investment in human capital formation, have been clarified. It has been shown that in the socio-economic development system of the country, the knowledge economy as a social labor resource is one of the most important criteria of efficiency of organization of the socio-economic system of the country. Preconditions for organization of innovative-educational sector of economy of the Russian Federation are stated. The article focuses on the strategic landmarks of the formation and development of the innovative-educational sector of economy in the Southern Federal District. Network integration is considered to be the factor which enables to treat education as a separate, innovational sector. As for the preferable form of its organization, the authors mention private-public partnership with attraction of businesses. The paper also covers technical characteristics of implementing the model in the innovative-educational sector of economy of the Southern Federal District. The article presents promising areas of the study of this problem, which involves further development of the theory of intellectual capital development in education, subject-oriented methodology of educational system modernization in the applied aspect, as well as technologies of management of the national innovation-oriented educational system of the Russian Federation.