This article examines the relevance of modernization of today`s education, in particular, the reform of activities in the management of educational organizations. Modernization of management of educational organizations involves the introduction of innovative approaches in the management of educational organizations. It was revealed that one of the priority areas that characterize the activities of modern educational institutions is the transformation of its management cycle. As one of the effective management methods, in contrast to the existing traditional vertical command-administrative system, is considered a horizontal-cyclical organizational structure (HCOS). This transformation has aimed to the implementation of decentralized coordination of the actions of the relevant organizational units (the formed departments) in the process of performing common tasks. The presented work will investigate the implementation of HCOS on the example of the Institute of Natural sciences and geography of the Abai Kazakh National Pedagogical University.