The author proves that in modern conditions the strategy of Russian Universities should be focused on a clear view of deep organizational and economic changes in the organizational system necessary for ensuring compliance with the University’s fast-changing environment instead of ambitious goals in the areas of their activity. The author presents the results of a critical analysis of the current system of adjusting the salary of academic staff using a variety of indicators. The paper argues that the University should not be predominantly influenced by the dececions of governing bodies. Instead, it should be focused on the interests of scientific, educational and innovative development of agriculture and rural areas of the region. A significant role should be given to employers and other beneficiaries of the outcomes of the University’s activities and their influence on the University management system. The author draws on some examples of such strategical behaviour of Russian universities and proves the necessity of changes in the system of academic staff motivation. Accordingly, he proposes that the number of qualification levels of the University academic and scientific staff should be increased and the evaluation criteria of each level should be determined accorfding to the University development strategy.