Subject. The article examines processes of import substitution in Russia and its regions within the framework of ensuring the economic security of the country. Objectives. The aim is to substantiate a methodological approach to determining the impact of innovative component of import substitution on the economic security of the region. Methods. The study employs the method of convolution and the index method. Results. We analyzed investment and innovation activity of organizations in recent years. Along with positive trends, we revealed a decrease in the share of organizations engaged in technological innovations in mechanical engineering and in the field of scientific research. To assess the impact of innovative component of import substitution on the economic security of the region, we determined the relative dynamics and convolution of innovation costs, investment volumes and innovative goods, exports and imports. We obtained estimated coefficients of indicators’ increase to achieve normative values of import substitution and economic security. We tested the methodology, using the mechanical engineering of the Sverdlovsk Oblast case. Conclusions. The presented methodological approach is universal and can be applied at the level of the constituent entities of the Russian Federation.