Accelerated development of eastern regions is one of the priorities of regional management. It is due to the significant role of Siberia as a “storehouse” of natural resources and a “centre” interconnecting the West, the East and the South of Eurasia. In order to improve the spatial development of Siberia, the South Siberian and Angara-Yenisei macroregions have been formed in the Siberian Federal District to ensure accelerated development of its territories. Interregional integration of macroregions, the main directions of which are interregional production clusters, joint investment projects, interregional associations, is proposed as a mechanism enabling the realization of the goals set. The novelty of the study is the comparison of economic potentials of macroregions and the substantiation of regional management tools for their interregional integration. The results of the study prove the effectiveness of the mechanism of interregional integration at the level of macroregions.