The article develops a methodology for managing the risks of economic security of a cross-border region in the context of asymmetric cross-border interaction on the example of the Amur region of the Russian Federation and the Heilongjiang Province of the PRC. The article analyzes the threats caused by the structural imbalance, raw material orientation and technological lag of the Russian side. The suggested methodology integrates quantitative and qualitative tools into a single algorithm of proactive management. For the first time, based on the synthesis of adapted methods of quantitative assessment and scenario forecasting until 2026, the article carries out a dynamic assessment, revealing an interconnected set of threats, such as declining economic sovereignty due to monocentric dependence on China, the crisis of the real sector, and critically low RD funding. The article provides a full-cycle risk management algorithm (diagnostics and monitoring) and a roadmap for 2025-2030 with threat minimization mechanisms: the creation of a cross-border innovation and production cluster and the massive introduction of the PDCA cycle in companies. The implementation of this approach will make it possible to move from a reactive response to strategic risk management, strengthening economic sovereignty by diversifying ties and stimulating innovation.