This paper shows the diversity and significance of relations of duality among different economic systems. The composition of the principles underlying the system economic theory used for the analysis of duality in the economy is investigated. The concept of the economic system is clarified and the equivalence of three basic concepts of the economic system is shown: a) as a space-time volume (“black box”); b) as a complex of elements and connections among them; c) as a tetrad, including object, project, process and environment components. In a new way, the concept of the tetrad is revealed. The actual interpretation of the interrelationships of its components, based on the mechanisms of intersystem circulation of spatial and temporal resources and the transmission of abilities from one economic system to another, is proposed. On the basis of the obtained results, the most essential aspects of duality in the theory of economic systems are considered. It is shown that the interaction of internal content and the nearest external environment of economic systems lies in the nature of the relations of duality. A new approach to modeling the structure and to functioning of the economic system, based on the description of its activities in the form of two interconnected tetrads (the first tetrad reflects the intrasystem production cycle and the second one — the external realization-reproduction cycle) is put forward. It is shown that the concept of duality in a system economy creates prerequisites for adapting the functioning of local economic systems (objects, projects, etc.) in a market, administrative and functional environments and, as a result, harmonizing the economy as a whole.