In the article, according to the positive and negative aspects of the development of high-tech sector, the author justifies a methodological approach to its formation and development. A feature of the author's methodology is the integration target-oriented and institutional approaches based on the theoretical concept of the triple helix «government-science-business». The author presents the functional model of formation and development of high-tech sector associated with a hierarchical structure of goals, resources and program activities of the institutional sectors in the model triple helix. The triple helix model of high-technology sector augmented by a mathematical formalization of reconciling the motivational capacities of the main institutional sectors of the triple helix. The author cites the results of studies of cross-sector interactions, including the migration of managerial personnel between the institutional sectors. This article was prepared under the support of RFBR grant № 16-06-00403 «Modeling the motivational potential multisubject industrial policy in the conditions of new industrialization».