<p>The Heilong-Amur River Basin (HARB), shared by China, Russia, and Mongolia, is highly sensitive to climate change and human interventions. However, how large reservoirs reshape flood risks remains insufficiently understood. Using a distributed VIC-Reservoir hydrological model driven by multi-source meteorological forcing datasets and coupled with the HEC-RAS hydrodynamic model, we assessed changes in runoff and flood characteristics under multiple CMIP6 scenarios. The model performed well, achieving a daily <i>NSE</i> of approximately 0.76 at mainstem stations, indicating reliable applicability in cold regions with complex hydrological regimes. Future climate change is projected to substantially intensify hydrological extremes. By 2075–2099, basin-wide annual runoff is projected to increase by approximately 9%–20% in the midstream and downstream reaches, and mean annual floods increase by up to 38%, particularly under high-emission scenarios. Flood amplification is most evident in the Zeya and Songhua rivers and along the downstream Heilong-Amur River mainstem (with flood-season flows rising by approximately 30%), whereas persistent water stress is expected to remain in the Mongolian headwaters, highlighting an uneven pattern of hydrological change across the transboundary basin. Although large reservoirs substantially mitigate future flood peaks and inundation areas, their regulation capacity is projected to decline progressively under continued warming. To characterize this temporal evolution, we used the flood regulation peak year (FRPY) concept to identify the approximate timing at which reservoir flood-mitigation capacity reaches its maximum before entering a sustained decline. At the Amure station, this transition is projected to occur around 2062 and 2058 under SSP1-2.6 and SSP5-8.5, respectively. Similar timing is found at other major reservoirs, collectively indicating an approaching window in which current regulation strategies will become insufficient. These findings highlight the urgent need for adaptive reservoir operations and institutionalized transboundary cooperation in the HARB, particularly among China, Russia, and Mongolia, to prevent escalating flood risks under climate change. More broadly, the FRPY provides a transferable indicator for anticipating infrastructure thresholds and guiding climate-resilient flood governance in other vulnerable transboundary basins.</p>