The article describes the organizational structures of Russian higher education institutions “Volga State Academy of Water Transport” and Czech universities VŠB Technical University of Ostrava - the differences and peculiarities of organization management system, as well as the content and form of the management process, controls, in which management process is carried out on the relevant functions aimed at problem solving and achieving goals. From this perspective, the management structure of the universities is represented as a system of optimal allocation of functional duties, rights and responsibilities, procedures and forms of cooperation between its controls and the people working in them, that is, perform certain functions on specific issues rests with the experts and each performer or control is specialized in performing certain types of activities.