Among mathematical disciplines, algebra stands out in that, regardless of the object nature, it analyzes the connections between them. This paper substantiates the legitimacy of using mathematical structures to formalize a structural approach to building the process of comprehensive student learning. It is shown that the language of mathematical structures and schemes dominating in mathematical modeling, discrete mathematics and the theory of computational processes is the basis for the accumulation of a variety of other knowledge. It plays an important role in the mastery of activity methods aimed at implementing interdisciplinary connections when studying various university courses by students of higher educational institutions through interaction in the information educational environment. This methodological approach to teaching students is, in general, an effective method of training highly qualified specialists, and also creates the prerequisites for individual attention to those students who show increased interest in creative independent scientific activity, which is impossible without the use of structuring skills and identifying general patterns of information flows.