The research substantiates the current role of regulating interregional migration in the Southern macroregion of Russia. The research aims to develop tools for optimizing interregional migration policy in the new coordinates of the southern macroregion of Russia. To accomplish this task, the authors examined the macroregion’s management system for reproducing human resources using social justice and economic efficiency criteria. The methodological foundation of this research is an integration multilevel approach, which enables the government to develop and carry out an efficient and equitable interregional migration policy. The research results in methodologically grounded and empirically verified solutions to the problem of optimizing the settlement system of labor and non-labor migrant flows. The scientific novelty of this research lies in validating a multilevel integration strategy for resolving migration issues, as well as tools for improving contemporary interregional migration policy in the developing Southern macroregion of Russia. The authors proved that the use of the developed toolkit makes it possible to achieve one of the key imperatives of effective (fair) regional policy—to identify the dominant factors of interregional migration in the development of the territorial socioeconomic system of the country, defining the “points” of influence of the state and adjust migration policy to them.