Freshwater reservoirs are widely recognized as methane (CH4) emission hotspots. Existing research has shown that temperature and hydrological conditions significantly affect wetland CH4 cycling processes. However, the feedback of the CH4 cycle to climate warming remains unclear for deep reservoirs where seasonal water thermal stratification exists. This study combined a reservoir CH4 cycling model and a Statistical DownScaling Model (SDSM) to evaluate reservoir CH4 cycling feedbacks under multiple climate change scenarios while accounting for hydrological uncertainty. Daily air temperatures in 2100 were predicted by the combination of the CanESM5 model and a SDSM. To address hydrological uncertainty, we selected three representative hydrological years (i.e., wet, normal, and dry) to create hydrological scenarios. Results showed that annual sediment CH4 production increased with warming, ranging 323.1–413.7 × 103 t C year−1 among multiple scenarios. Meanwhile, the CH4 oxidation percentage decreased with warming, which meant warming promoted sediment CH4 release non-linearly; 67.8–84.6% of sediment ebullient flux was ultimately emitted to the atmosphere (51.3–137.7 × 103 t C year−1), which showed ebullition was the dominant emission pathway. Higher air temperatures and drier conditions generally promote reservoir emissions. This study is helpful for predicting reservoir emissions while directing decision-making for reservoir sustainability.