This article discusses the main concepts of the inter-organizational cooperation model, inter-organizational accounting and analytical system and the role of control in the management accounting system of partners. The main objective of the research is to build a management accounting model of enterprises at the inter-organizational level, which operates on the basis of self-organization and takes into account different levels of interaction of the enterprise. The management accounting model focuses on the role and place of control in the complex structure of relationships between enterprises and partners in the framework of inter-organizational management accounting. The control element is an important part of building a fundamentally new inter-organizational accounting and analytical system. This is due to the complexity of this structure, the presence of an unlimited number of subjects of inter-company relations and management levels. Establishing an effective control system will prevent a conflict of goals between partnership subjects, balance the interests of partners, and carry out coordinated adoption and implementation of decisions on the functioning and interaction in the network.