The article describes the methods of organizing industrial relations and the system of managing the economic processes of innovative transformations. Based on the generalization of the provisions of the organization theory and management theory, the methods of organizational and reengineering are ordered into an integral system with clearly defined characteristics, a logical structure and a process for their implementation. The features of the transformation of the control system of such a complex functional and technological formation as a production system are considered. It is noted that it is a synthetic multidimensional phenomenon, which is characterized by three attributive dimensions of the production system: process dimension, object and subject dimensions. It is substantiated that the integration of dimensions provides an opportunity to analyze, study and design a more efficient production management system based on organizational reengineering methods, as well as the opportunity to obtain functioning models focused on an object, formation or practical implementation. It is shown that industrial relations can be of a diverse nature, therefore, when conducting organizational reengineering of the management system, it is necessary to consider managerial, social and economic relations. The most significant factor in these relationships is the level of the management hierarchy, that is, the management environment. It can be divided into what directly controls (influences) and what controls indirectly or regulates. It is substantiated that the control system must ultimately be constantly improved and adapted to the changing conditions of the enterprise's production base. The requirements that the system of managing the economic processes of innovative transformations must meet in the framework of the ongoing technological rehabilitation are formulated. Key words: methodology, organizational reengineering, industrial relations, economic processes, innovations, management system, flexible production systems.