The state of modern economy is exposed to significant challenges from geopolitical risks and transformation of the process of industrial development, which requires determining the conditions for implementing modern industrial policy and changing directions and priorities of industrial development. Improvement of the ways of production, development of the system of social institutions takes place when solving the issues related to the development of science underlying the formation of new industries. The subject of the study is the transformation of industrial policy features in modern economy at various levels of interaction between government and business. The article examines the changes in industrial development and corresponding transformation of industrial policy tools in import substitution development. The study aims at determining the relationships between the directions and levels of implementing industrial policy in accordance with system analysis and identifying the key features in the relationship between business structures and the state. The theories of industrial development and the concepts of resource and process approaches to industrial development and implementation of innovative industrial policy provide the methodological basis of the study. The study uses the methods of system analysis and synthesis in identifying the key relationships between business structures and the state in achieving the goals of industrial development. The study defines the transformation of types, tools and system of indicators of industrial policy under the sanction pressure on the economy, identifies the possibilities of using the matrix system in managing industrial development, implemented at three levels (macro-, meso- and microeconomic) in interaction of business structures and public authorities, assesses the possibility of forming and conducting conservative industrial policy in the lack of scientific research funding. The findings can be used in assessing the priorities, directions and transformation of the tools used to implement an innovative model of industrial policy in the Russian economy, in the development of import substitution and formation of new industries, to form an effective interaction of innovation process and the process of industrial development of the national economy.