The article considers the concept of system economy as a direction in economic theory based on the generalization of neoclassical, institutional and evolutionary theories, which is based on a combination of processes of creation, functioning, interaction and transformation of economic systems. Approaches to understanding the category of economic system, which covers the processes of production, distribution, ex- change and consumption of goods, as well as the relationship between producers and consumers of material goods and services are generalized. It was argued that the economic systems functioning structure and mechanism is based on cybernetic, informational and organizational theoretical principles of general systems theory. Having considered the scientifc directions of general systems theory, synergetics, change theory, catastrophe theory etc.,it was proved that isoformisms is manifested not only as similarity or clear correspondence of systems construction, but as commonality in their functioning and development as well. It was substantiated that a complex economic system has an emergent synergetic behavior and its development is based on non-equilibrium deviations of critical bifurcation points. It was revealed that complex economic systems have high uncertainty of behavior and their strategic development is focused on the search for self-development ways and unrealized reserves which results in a qualitatively new state of the system. Innovations and sustainable development principle were proved to be the main factors of violations in the agri-food systems sustainability and achieving their balanced socio-ecological and economic development. The negative and positive impact factors influencing the sustainability of agri-food systems modern development are systematized. These factors must be taken into account when substantiating the options for the systems development on the basis of targeted management influence. The paper highlights that agri-food systems operate in a multilevel environment and identifes strategic priorities for their development at the micro, meso, macro and mega levels. It is emphasized that agri-food systems affect the development of rural areas and they can ensure the homeostatic systems. The defnition of the category "agri-food systems" is extended and their specifc features, development trends, challenges and threats in achieving the sustainable development goals are generalized. Key words: economic system, agro-food system, rural areas, sustainable development, innovation, globalization.