The work is devoted to the selection of key performance indicators (KPI) of universities, as well as the development of the concept of using these indicators in assessing the effectiveness of universities in the scientific and innovative sector of Russia. The study used a combination of descriptive and deductive methods, as well as experiment.There were analyzed the data on financing, the number of publications indexed in the Web of Science, as well as the number of employees of 14 Russian universities that have been participating since 2013 in the state program "Project 5-100". This program is aimed at the adaptation of Russian universities to international standards and incorporating them into international education environment. A system-dynamic model is constructed that allows, on the basis of the key performance indicators, to find new approaches and ways to achieve the goals set and to build an effective university development strategy in the transition to a digital economy.