The authors of this article are carrying out the analysis of the students’ training programs congruence to the sectoral structure of employment in 84 Russian regions using the sectoral model concept and the index of structural differences. The paper presents a methodological approach to assessing the congruence of training programs with the needs of the regional labor market in Russia. The level of regional higher education systems differentiation, the sectoral structure of graduates, and the level of their employment in the regional context were determined applying economic and statistical methods. The ratio of the graduates’ supply to their demand analyzed, there is presented a classification of regions according to the levels of this ration, conclusions drawn on the balance of higher education systems in the regions, taking into account the needs for training. A structural and professional disproportion between regional labor markets and regional systems of higher education in most regions of Russia is diagnosed, as well as a number of imbalances concerning specialists’ training in the secondary sector of the economy, which is decisive for the development of high-tech in dustries and provides the need for personnel within the new digital economy. The directions for overcoming dysfunction of the relationship between universities and the labor market are identified. The results of the study make it possible to make decisions on improving the policy of distributing the planned contingent of students by training programs in accordance with the needs of regional economies.