Aim. This study aims to examine consistent patterns in the formation of interdisciplinary and interregional interactions within multi-level socio-economic structures. Methods. The author’s theoretical and methodological paradigm is expressed in a concept of strategic competitiveness management for the Russian agro-food complex. This study employs data provided by the Federal State Statistics Service, OECD, and the Research Institute of Agricultural Problems of the Russian Academy of Sciences, which serves as the statistical basis for the study. Results. We provide the fundamentals of the management of interdisciplinary and interregional interactions within multi-level socioeconomic structures using modified input-output models. We also demonstrate the existence of invariant parameters of such models, which allow for examining interdisciplinary complexes as relatively autonomous objects of strategic innovative management. We also demonstrate that the substantiation of a program for ensuring food security of a country and modernization of interdisciplinary interactions management within multidisciplinary structures of the agro-food complex proposed by the author can be implemented.