In this article a problem of congruence of university structure, modes of knowledge production and the G. Beytson’s theory of learning are considered as the research goal. This prob¬lem is considered for the first time. The methodological basis of work is the theoretical-empirical methods of scientific knowledge, including the methods of idealization, modeling and comparison. In the center of consideration there is a university, a unique institution which accumulates in it education, researches (science), and innovation’s production. The structure of university constantly changed according to the requirements of society. The author of this article considers that the university has to represent a modern scientific, educational and industrial complex with the academic kernel and the interdisciplinary project-oriented periphery. This periphery has to include two interuniversity components: profession-oriented modules (POM) and project-innovative fields (PIF). Through these components the university interacts with business. This interaction is promoted by the small innovative enterprises, the scientific-educational centers and other innovative structures which are already created in some countries. Successful innovative activity demands modern modes of knowledge production. Evolution of these forms from the Conception of traditional disciplinary-organized knowledge production (Mode 1) to the Conception of knowledge production «Penta Helix» (Mode 5) is investigated in this article. A widely known model «Triple Helix» of Henry Etzkowitz (Mode 5) is also considered. These modes of knowledge production are correspond to well-known learning levels of Gregory Beytson. Prof. Beytson has predicted the existence of 5 learning levels (from 0 to ΙV), but only three of them (Ι, ΙΙ, ΙΙΙ) are actual for the modern person. Learning Ι is the development and improvement of new receptions and abilities. Learning ΙΙ is a fruitful in the time of fast, sharp changes. It supposes instant reorganization of absolutely other category or a class of actions. Such learning is effective in the time of fast transition to new policy, to new values or priorities. Such learning is rather innovative. Only the solution of the problem of congruence of knowledge production and learning levels will allow university to execute successfully its new mission – innovative.