The author in this article considers the basic concepts of the model of inter-organisational cooperation, accounting and analytical system and the role of control in the management accounting system of partners. Inter-organisational cooperation is a system of organisational, functional and technological relationships of business entities united by common mutually beneficial goals, which are achieved through the synergistic effect of partnership at a high level of business culture, voluntariness and trust. The elements of such cooperation include: the process of inter-organisational interaction; subjects and objects of organisational interaction; methods, tools, products; level of interaction; cooperation support.