The importance of this study is due to the need for increasing the performance and efficiency of management of structural changes in Russian industry and regional industrial complexes in connection with forming and implementing the industrial policy at the national and the regional levels, increasing the number of instruments of industrial policy, implementing import substitution plans, as well as forming a system of strategic planning and activities of development institutions. The aim of the study is to identify the trends of structural changes in the manufacturing industry at the national and regional levels prior to adopting a new regulatory framework of industrial policy in the Russian Federation, as well as quantitative and qualitative analysis of structural changes in the new institutional conditions. The objectives of the study are identifying the trends, quantitative and qualitative assessment of structural changes in the industrial complexes of the Russian Federation and Kostroma region; describing the industrial policy instruments aimed at implementing structural changes at the national and regional levels. The research methods used are the method of economic analysis and the geometric method. We have considered the existing problems in the management of structural changes in the industrial complex. We have analyzed the structural changes in the manufacturing industry of the Russian Federation and Kostroma region in 2010-2015, using the geometric method and the method of economic analysis. For integral evaluation of structural changes in the manufacturing industry of the Russian Federation and Kostroma region, we have designed and constructed the vectors of changes in the branch structure of the manufacturing industry by volume of shipped goods produced within the region, works performed and services rendered, and the volume of investment in fixed capital. We have identified the main trends, highlighted the periods characterized by the most intensive structural changes, and provided a quantitative and qualitative assessment of these changes. The results of the analysis of directions of structural change are compared with the results of the analysis of using the tools of modern economic policy with the aim of implementing structural changes in the industry. We have described the tools of investment and industrial policy of the Kostroma region in 2016. The obtained results can be used for forming an industrial policy of managing structural changes, estimating the impact and effectiveness of structural changes in the industry. The directions for further research can involve analyzing structural changes in the industry in different regions and evaluating the effectiveness of structural instruments of industrial policy at the national and regional levels.