Abstract: Unlike conventional flood detention and storage areas that are primarily designed to attenuate downstream flood peaks and protect downstream regions, the Xiaoqing River flood detention and storage area primarily serves to safeguard key upstream areas of Beijing. Its operation simultaneously transfers floodwater and associated risks to the detention area and downstream confluence zone, thereby requiring coordinated consideration of upstream flood safety, the storage capacity of the detention area, and downstream flood responses. To address these specific operational requirements, a coupled one-dimensional and two-dimensional hydrodynamic model was developed and validated using observed data from the downstream Dongci Village hydrological station. Under a 100-year flood scenario, six gate-operation schemes were designed to systematically investigate the effects of the coordinated operation of the flood diversion gate, river-blocking gate, and drainage gate on inundation responses within the detention area, flood-volume redistribution, and downstream inundation.The results showed that: (1) The Nash–Sutcliffe efficiency coefficients for the simulated water level and discharge were 0.75 and 0.80, respectively, indicating that the model could satisfactorily reproduce water exchange between the river channel and floodplain and the overall flood-routing process. (2) Under the operational scenario prioritizing flood protection for key upstream areas of Beijing, the coordinated operation of the river-blocking gate, flood diversion gate, and drainage gate enabled stage-specific regulation, characterized by active flood diversion and storage during the flood peak and sustained drainage after the peak. Compared with the scheme involving only the river-blocking gate and flood diversion gate, the three-gate operation reduced the peak inundation volume, maximum inundated area, and mean inundation depth in the core detention area by 9.26%, 3.00%, and 4.18%, respectively, while achieving a total drainage volume of 18.1608 million m3. Meanwhile, the peak inundation volume in the downstream confluence zone increased by approximately 0.25%, and the peak occurred 1 h later, indicating that improved drainage from the detention area may be accompanied by enhanced downstream backwater effects during the post-peak stage. (3) The flood diversion gate played the dominant role in transferring flood risk from upstream areas to the detention area. The river-blocking gate improved flood diversion efficiency by modifying the hydraulic boundary conditions, whereas the drainage gate primarily enhanced post-peak drainage efficiency, with a more pronounced effect when operated jointly with the river-blocking gate. (4) Inundation in the downstream confluence zone was jointly affected by tributary inflows and downstream water levels, showing a slight decrease during the rising stage but a slight increase after the flood peak. This indicates that, although the proposed regulation strategy improves upstream flood protection and facilitates post-peak recovery of the detention area, it may also prolong downstream drainage and intensify localized backwater effects.This study elucidates the coordinated regulation mechanisms of multiple gates under the objective of protecting key upstream areas and provides technical support for optimizing gate-group operations in unconventional flood detention and storage areas and for coordinating regional flood-risk management.