The Russian agro-industrial complex is characterized by significant interregional differences in the growth rates of production, the level of labor productivity and the efficiency of land use, these trends determine the need for state regulation of territorial aspects of its development in accordance with the principles of the Spatial Development Strategy of the Russian Federation until 2030. The main tasks of the spatial development of the agro-food complex include the formation of a balanced territorial organization of the economy, aimed primarily at making better use of the agricultural potential of the territories. The purpose of this paper is to form a basic system of indicators and its application for the analysis and forecasting of the balance of the territorial organization of regional agricultural systems. It is proposed to identify a number of stages in solving this problem: conducting interregional comparisons of indicator values; assessing the potential of territories; identification of directions for increasing the efficiency of using their potential and ensuring innovative development. Interregional comparisons were conducted using the example of four regions. Results shown that in order to assess the territorial balance of the agro-food complex, it is necessary to use indicators of the growth rate of production of the most important types of products, the availability of material resources, the quality of life of rural people, and food consumption by the population of the regions.