The object of study is a change in the organizational management structure (management system) under the influence of factors of the internal and external environment (concept factors). The subject of the research is the methodology and sequence of logical-linguistic (semantic) modeling to establish a connection between groups of factor concepts and assess their impact on the system of organizational transformations. The applied research methods: constructing a qualitative model of system dynamics in the form of a graphic diagram, a cognitive modeling method for weakly structured systems, a dynamic and static analysis method, a fuzzy mathematics analysis method, a Pearson (r-Pearson) linear correlation coefficient scale, a method for constructing a cognitive map by V. B. Silov (1995), a method for constructing a consonance matrix based on data from logical-linguistic (semantic) modeling. In the process of research, a methodology has been developed for the sequence of constructing a logical-linguistic (semantic) model based on the disclosure and impact of factor concept groups on changing the system of organizational and managerial transformations, with their further consideration in changes in the organizational management structure. The developed methodology allows defining the intensity of the relationship between groups of factors of the external and internal environment that affect the system of organizational transformations.