The relevance of the study is determined by the necessity of transition of the Russian economy to a new model and a new quality of economic growth, which is possible through introducing structural reforms in the economy, and is a component of economic development. The purpose of the study is in developing methodological and procedural foundations for estimating the quality and efficiency of structural changes in the economy. The objectives of the study are to give a brief evaluation of the industry in the Kostroma region as a control object of structural changes; to formulate the principles of structural changes management in the economy (industry); justify the selection criteria of the purpose, methods, and tools to manage structural changes in the economy (industry) and requirements for the subjects of management of structural changes; develop principles, criteria and indicators for assessing the quality of structural changes in the economy (industry); to propose criteria and system of indicators of an efficiency estimation of structural changes management in the economy (industry) for the controlled and controlling systems. The research methodology is based on a systematic approach. The method of study is economic analysis. It is possible to allocate the following features of the conducted research and the results obtained: principles, criteria and systems of indicators were developed on the basis of the principle of consistency as a core of system philosophy; the author offers a system of indicators to assess structural changes in the object, project, process and environmental systems on the basis of the classification of economic systems proposed by Kleiner; the structural changes themselves are considered as process and project systems with the appropriate features and specifications; the industrial complex as control object of structural changes is also considered as a set of systems of different types. The methodology and procedures for assessing the quality and effectiveness of the management of structural changes in the economy should act as a support for achieving the goals of state development programs and for improving the efficiency of state management of the economy of the region. Continuous monitoring of structural changes in the economy of the region and its industry will allow to timely identify structural problems and their aggravation, and to direct the available resources to resolve these problems. The proposed methodology and procedure will provide a systematic management of structural changes in the economy and industry of the region. The scope of application of the obtained results is the structural policy, the management of structural changes in national, regional economy, economic complexes, industry.