Carrying out large-scale structural transformations of both the entire Russian economy and its individual actors is one of the most important tasks of the current stage of national development. The urgency of this problem has increased dramatically during the COVID-19 pandemic. The purpose of this paper is to identify the most significant factors in the pandemic that affect the economic growth of Russia's regions and reduce territorial inequality. The use of methods of comparative and economic-statistical analysis made it possible to establish that the most important independent factor in the development of a region is the structure of the economy and such a factor that ensures it as the regional structural (industrial) policy. It has been substantiated that structural modernization is the basis for pursuing a non-contradictory short- and long-term policy to reduce interterritorial inequality. A particularly negative impact of the pandemic on regions with a low level of development of the real sector and overdevelopment of the service sector has been revealed.