In this article, we substantiate the high relevance and practical importance of research in the field of creating a methodology of structural identification for the design of automatic control systems with the required properties. In particular, we give a brief description of the current state of scientific knowledge about structural identification. Secondly, we formulate the problem statement of the methodology of structural identification. We reveal the basic content of the key concepts of this methodology. In particular, we develop the reference model of the subject’s behavior of the rational structural identification.