The article is devoted to the analysis of the risks of transition to a nonlinear model of higher education, which appears to be a necessary prerequisite for the formation of the system of higher education in the macro-region. The study allowed to do the following: 1) look at the proposed nonlinear model of higher education from a critical point of view; 2) identify the problem areas of transition to the new model; 3) create a basis for the development of strategies and methods for their minimization.