Substantial nutrient inputs resulting from reservoir impoundment typically increase sedimentation rate and primary production. This can greatly enhance methane (CH4) production, thereby making reservoirs potentially significant sources of atmospheric CH4. Consequently, elucidating CH4 emissions from reservoirs is crucial for assessing their role in the global methane budget. Reservoir operations can also exert a considerable influence on hydrodynamic and biogeochemical processes, potentially leading to pronounced spatiotemporal heterogeneity, especially in reservoirs with complex tributaries, such as the Three Gorges Reservoir (TGR). Although several existing studies have investigated the spatial and temporal variations in CH4 emissions in the TGR and its tributaries, considerable uncertainties persist regarding the impact of reservoir operations on CH4 dynamics. These uncertainties arise primarily due to the limited spatial and temporal resolutions of previous measurements and the complex underlying mechanism of CH4 dynamics in reservoirs. In this study, we employed a fast-response automated gas equilibrator to measure the spatial distribution and seasonal variations of dissolved CH4 concentrations in XXB, a representative area largely impacted by the operation of the TGR and known for its severe algal blooms. Additionally, we measured CH4 production rates in sediments and diffusive CH4 flux in the surface water. Our multiple campaigns suggest substantial spatial and temporal variability of CH4 concentrations in XXB. Specifically, dissolved CH4 concentrations were generally higher upstream than downstream and exhibited a vertical stratification with greater concentrations in bottom water compared to surface water. The peak dissolved CH4 concentration was observed in May, corresponding to the drained period. Our results suggest that the interplay between aquatic organic matter, which promotes CH4 production, and the dilution process induced by intrusion flows from the mainstream dominates this spatiotemporal variability. Importantly, our study indicates the feasibility of using strategic reservoir operations to regulate these factors to mitigate CH4 emissions. This eco-environmental approach could also emerge as a pivotal management strategy to reduce greenhouse gas emissions in other reservoirs.