The management system of inter-organizational relations between ATP and partners has been improved, which is formed on the basis of the apparatus of cybernetic modeling of viable systems, as well as the use of structural modeling methodology SADT. The methodological basis for assessing the level of inter-organizational relationships of ATP with individual partners, which, unlike existing ones, is based on the use of the generalized Harrington desirability function, as well as the radar method to assess the generalized indicator of the relationship between ATP and partners, has been further developed. The methodological provisions of the assessment level of inter-organizational relationships of ATP with partners in the network based on the definition of strategic synergy have been further developed .