The article considers the concept of economic security in accordance with the provisions of the Strategy for the Economic Security of the Russian Federation for the Period up to 2030. The urgency of the intellectual migration problem for the regions and its influence on the economic potential of the state entity are emphasized. Today, the issues of reducing labor resources and high rates of the growing migration outflow of the population, which threatens the economic security of the region, acquire special significance for the modern research. Ensuring the regional economic security is possible under the condition of purposeful interaction of the forces and means capable of resisting threats, one of which is the migration outflow. There have been analyzed the statistical data of migration processes, of the labor market and the number of registered organizations and enterprises in the region in the case of the Astrakhan region, proved the impact of migration outflow on the innovation and economic security of the region. There are presented the diagrams of the structure of the leaving population aged 14 and older in the regional context of the Southern Federal District in 2019; migration growth of the population aged 14 years and older with higher professional education by the regions of the Southern Federal District in 2019. A graph of the growth rate of inventive activity over 2015-2020 has been illustrated. A diagram of the number of registered organizations, the growth rate of their number, as well as the average annual number of people employed in the economy of the Astrakhan region in 2018-2020 has been built. The correlation analysis of the probabilistic relationship between two variables - the indicators of the innovative sector of the economy and the number of enterprises and organizations in the region - has been carried out. The conclusions show the objectivity of the migration outflow impact as a threat to the economic security of the region, the need to ensure control over intellectual migration.