Reservoir operation policies affect sediment methane (CH4) production and pathways through complex influence on hydrodynamic and biogeochemical processes in reservoir water and sediment. However, the underlying influencing mechanisms, especially the impact of operations on sediment CH4 production and pathways, remain poorly understood. This study combines a physical‐biogeochemical model with a reservoir operation model to evaluate operation impacts on spatiotemporal sediment CH4 production and release dynamics and to analyze affiliated processes and driving factors. Three typical operation policies (i.e., standard, hedging, eco‐friendly) are selected to create the operation scenarios, and a coupled physical‐biogeochemical model is adopted to simulate and compare sediment CH4 production, consumption, diffusion, and ebullition under these scenarios. The methods are applied in the second largest reservoir in China (i.e., Danjiangkou Reservoir) as a case study. Results show that annual total sediment CH4 production among the scenarios ranges from 285.9 to 298.3 Gg C year−1, while operation scenario outcomes significantly differ. Specifically, a significant CH4 percentage (34%–39%) is oxidized in surface sediment while the remaining escapes sediment through diffusion and ebullition. Although diffusion accounts for >60% of the annual sediment CH4 release, sediment ebullition ultimately dominates atmospheric CH4 emissions. Annual total atmospheric CH4 emissions range from 42.8 to 71.1 Gg C year−1 and account for 14%–25% of the annual total sediment production among the three scenarios. The differences demonstrate that reservoir operations significantly impact CH4 pathways and atmospheric emissions. This study provides implications for reservoir managers to coordinate socioeconomic and ecological protection while mitigating CH4 emission targets.