The significant increase in the influence of innovation and information technologies in the modern world, including on economic processes, their constant interaction with classical markets of production factors, and accordingly the need to develop a methodology for assessing their mutual influence - all this has determined the purpose and tasks of research. The article discusses the features of markets mutual influence of innovation and information technologies, as well as their impact on the economy of the region. Based on the conclusions, a methodology for quantifying this influence is proposed, which is characterized by simple and convenient application in the implementation of state regulation of the regional economy. The study is based on the analysis of statistical data for more than 20 years of the economy development of the Russian Federation and the Republic of Tatarstan and is highly representative. The results of the study allowed justifying the theoretical approach, to develop methodological and practical recommendations on diagnostics, assessment and forecasting of the impact of the two most important components of the modern industrial revolution 4.0 - innovation and information technologies - on the stability and balance of the regional economy. The main product of the study is the system functional multi-sector model of the regional economy, which allows solving all the above-mentioned problems and problems in an optimal way.