This study examines the state management of integration processes in the Union State of Russia and Belarus, focusing on the formation of a unified scientific and technological space in the digital era. Despite extensive research on Russian-Belarusian integration, there remains a significant gap in understanding the specific challenges and opportunities presented by scientific and technological integration in the digital age. The research aims to identify key challenges, opportunities, and strategies for enhancing cooperation and innovation within this framework. Employing a mixed-methods approach, the study analyzes data from official statistics, policy documents, and expert opinions. Key findings reveal significant disparities in innovation output, with Russia outpacing Belarus in patent applications (25,188 vs. 980 in 2022) and innovation density (251.6% higher). The research also identifies a strong positive correlation (r = 0.97) between Russia’s share in Belarus’s foreign trade and investments, indicating deep economic ties. Challenges include economic disparities, regulatory inconsistencies, and uneven digital development. However, joint initiatives in space research, IT, and digital development demonstrate a commitment to integration, with a balanced distribution across sectors (28.6% each in digital/IT, medical/health, and education). Recommendations include addressing innovation disparities through targeted programs, harmonizing regulatory frameworks, and strengthening institutional support for collaboration. The study proposes a comprehensive strategy to leverage digitalization for integration, including developing common data sharing platforms and e-government services. This research contributes novel insights into the complexities of forming a unified scientific and technological space within a supranational entity, offering valuable guidance for policymakers and researchers in the field of international integration and innovation management.