Under modern conditions of turbulent external environment, one of the reserves for increasing the efficiency of an enterprise’s economic activity is its involvement in joint activities with other enterprises, which together form a large-scale economic and production system. The author’s hypothesis in this case is to consider efficiency as a function of the ability of participants in a large-scale system to establish appropriate communications. Accordingly, the shortcomings of communication of participants in a large-scale system are determined by the main factor of stability loss of the economic-production system. The aim of the article is to develop the theoretical and methodological bases for ensuring an increase in viability of large-scale economic-production systems through optimizing the links between its participants by the criterion of compliance with structural and communication stability. In the framework of achieving the aim of the article, the relevance of introducing the concept “structural and communication stability” of an enterprise is proved, and its essence is substantiated. To identify the factors of stability loss, there used recommendations from the body of knowledge on system engineering regarding the construction of a hierarchy (holarchy) of a complex system, for each level of which the factor of stability loss is determined. A reference model for establishing communication between participants of a large-scale system is developed, and the possibility of detailing such a model by means of multi-agent modeling is provided for detailing the parameters of interaction between participants of a large-scale economic production system. The application of this model is the basis for ensuring the stability of the economic system by forcing internal and external stakeholders to fulfill their functions.