In Russia, all the regions are initially considered economically and socially complex systems that develop along the path of a huge set of conditions and processes arising in the internal and external environment. In my opinion, these types of processes should include limitations and resource opportunities, various changes in society, areas of development of the institutional area of the formation of environmental factors, processes and phenomena in the production of non-material, as well as, most importantly, of a material nature. It should be noted that the main and most important basis of the material base studied by me is the economic structure of the regional ecological system of the region, which to a greater extent characterizes stability and its ability to dynamically develop, improve the region as a whole, and its individual territories in particular, through the identification of the input flow and the values and results obtained at the output. It is important to focus attention on the fact that all economic and ecological systems in the process of their development at various stages of evolution are predominantly of the inertial type, which indicates the lack of development of a scientifically based system characterizing these states. In this regard, there are many global issues, both from a scientific point of view and from a practice-oriented direction. Thus, the author in this article examines the issues of methodological analysis and critical criteria explanation of the methodology of comprehensive assessment of the ecological state of the city of Ufa of the Republic of Bashkortostan in its close relationship with economic systems and structures.