Institutional modeling is, at first glance, a rather well-known trend in modern economic theory and institutionalism, however, despite the development of various econometric models, the models of institutions have characteristics associated with the object of modeling. This requires the formulation of general principles and the systematization of different approaches in the field of modeling in order to overcome the internal difficulty of creating the model of institutions and their changes; to divided the created models into groups and types; to define their field of application and improvement, practical use. To do this, the author uses different analogies, the aggregate approach, evolutionary modeling, and others. The article shows the possibilities and limitations of various approaches to the modeling of the institutions, in particular, evolutionary models. The approaches to the modeling of functions and dysfunctions used to study the interaction of agents and institutions are summarized. As a part of the modern Russian institutional school, it is possible to distinguish a system-aggregative direction of the modeling of institutions (Makarov-Kleiner-Polterovich), which consider both an enterprise and the institutional reforms at the system level with a significant number of parameters. We also can allocate micro-institutional direction (E.V. Popov et al.), which consider a specific state of institutions and instrumental ways of influencing to change these states having a considerable practical importance. The functional structure is important in the framework of both approaches, especially the violation, destruction or loss of functions – reduction of their quality, etc. According to one of the control functions, the descriptive model of coordination dysfunction with a possibility of its use in the analysis of macro-management is given.