The modern stage of modernization of both the national and the world higher education system necessitates the transformation of higher education institutions into entrepreneurial, innovatively active organizations that are able to quickly adapt to volatile changes in the external environment. In this regard, many issues require a new solution regarding the management of higher education institutions (HEIs), i.e.: ensuring the quality of higher education, training the personnel, appropriate to labor market, providing various educational services, ensuring the continuity of education, and improving the organizational and economic mechanism of management of HEI. From the point of view of the system approach, a HEI is seen as an open system, a mechanism for converting input information or resources into final products, where effective organization of internal processes becomes one of the most important ways to obtain its competitive advantages. Based on the analysis of the main properties of HEI as an open dynamic system, it is defined that the most important systemic characteristic of university is its organizational structure, which includes four main aspects: description of the structure of subdivisions and departments; connections between them and the external environment; information circulating on these connections; functions performed by structural units and departments. The article is aimed at studying various types of organizational structure of management of higher education institution, determining the specifics of their application in the activities of the university, which operates in an open informational and educational space. The main types of organizational structure of management of HEI, built on the classical principle, are distinguished; weaknesses and strengths of their application for the management of HEI are determined. It is proved that the organizational management structures, built according to divisional and matrix types, are promising, since only they are able to adequately and promptly respond to changes both in the internal and external environment of HEI. A list of requirements to meet the contemporary, effective organizational structure of a higher education institution is formed, the highlighted requirements are: optimality, operational efficiency, reliability, economic efficiency, flexibility and stability of the management system. The carried out study allowed to conclude that a higher education institution in the process of its life cycle should timely adjust its strategic goals of activity and make adequate changes to the organizational structure in accordance with the new conditions in which it functions.