A strategy for quantitative analysis of mono- and polysystemic organization of multi-level geospaces is described, with the construction of a series of empirical models of inter-component and inter-complex connections. The “micro-” and “macrosubstrate” approaches to the structural and functional analysis of the state of the natural environment are combined. As a methodological basis, a provision on the structural levels of natural-territorial organization is proposed, based on the conceptual cybernetic model of the natural complex as a hierarchical control system. A cybernetic model of the natural complex has been created as a hierarchical control system; the model has enriched modern ideas about the mechanisms and structural levels of the spatial organization of the natural environment. Model has enriched modern ideas about the mechanisms and structural levels of the spatial organization of the natural environment. An experiment was performed in order to analysis the state of geographical spaces by three blocks of cybernetic model: landscape frame, processor, and landscape pattern. Based on this model, a system of conjugation of different-level characteristics of natural components with the taxonomic rank of geographic spaces (from the geographical sector and natural zone to landscape facies and biogeocoenosis) was constructed. Using the Volga River basin as an example, a comparative assessment of environmental factors in their landscape-forming influence was carried out.