The research urgency is caused by necessity of planning regulation of higher education development at all levels of management. The purpose of this article is to develop the structure of a control system of higher education development, the Foundation of which is understanding of the quality of higher education as factor for development of the system and reconcile of the education agents' interest. Based on the definition of levels, types of control and methods for subordination, the authors have developed an innovative governance structure with the development of higher education system, including: a set of agents of higher education system; a set of relations between entities of management of higher education's development; the sequence and dynamics of functioning; criteria for management of higher education system; a set of normalized states for agents of higher education; the level of awareness of higher education agents in making managerial decisions. This article is intended for researchers and specialists in the field of development of higher education.