The input of large quantities of organic carbon sources from the land, and the discharge of carbon sources such as CO₂ and CH₄ caused by the operation and damming in the Three Gorges Reservoir Area have become the hot spots of recent research. In order to reveal the variation characteristics of CO₂ and CH₄ concentrations in different flow levels in the Three Gorges Reservoir Area, this study took the middle reach of the main stream of the Three Gorges Reservoir as the research objects. Samples were taken from Zhongxian County (ZX), Wanzhou (WZ), Fuling (FL)monthly from August 2017 to November 2018 to analyze and study the characteristics of CO₂ and CH₄ fluxes at the water-air interface under different operating conditions. Results showed that during the research period, CO₂concentration of the ZX, WZ and FL was between 0.008 6 mmol/L and 0.115 3 mmol/L, 0.003 5 mmol/L and 0.116 8 mmol/L, and 0.006 3 mmol/L and 0.098 6 mmol/L, respectively. The concentration of CO₂ at these three sampling points tended to be consistent and reached its peak during the drain period from April to May and its lowest point in the low water level operation period from June to September. CH₄ flux exhibited the feature of a sink during the operation at a low water level, but at FL it reached the maximum value as a source in the discharge period. The CO₂ fluxes at the three locations showed the feature of a source during the discharge period, but during low water level operation period, CO₂ flux indicated the switch between a source and a sink. CO₂ flux was at a medium level and CH₄ flux was at a lower-middle level compared with those of other reservoirs in the world.