The article is devoted to the issues of modeling the economic processes of ontogenesis that arise in the universities of a new formation. The aim of the study is to substantiate the subject area and build a mathematical model of the economic ontogenesis of a higher educational institution of a new level, the specificity of which is the fact that an educational institution has the opportunity to become an integrator, a kind of platform for ensuring economic superiority at the regional and global levels. The subject area of the model is based on the concepts and methods of the theory of innovation. The activities of the university are considered in three spaces: the space of knowledge, the space of consent and the space of innovation. Using the methods of the theory of fractional differential equations, a continuous economic and mathematical model has been built, which, at certain values of the input parameters, has a unique solution and correctly correlates with the experimental data. The proposed model is the main element of the multi-criteria model of interaction between the university economy and the economy of the region.