The input of much organic carbon sources from the land, as well as the discharge of carbon sources such as CO2 and CH4 caused by the operation of the Three Gorges reservoir area, have become the hotpots 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 takes 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 analysis 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, CO2 concentration of the ZX was 0.0086-10.153 mmol/L, while WZ was 0.0035-0.1168 mmol/L and FL was 0.0063-0.0986 mmol/L. The concentrations of CO2 at these three sampling points tended to be consistent. CO2 concentration reached the highest point during the drain period from April to May, and fell to the lowest point in the low water level operation period from June to September. CH4 flux represented “sink” druing low water level but FL reached the maximum value as “source” in the discharge period. Three locations were “source” of CO2 flux during the discharge period. During low water level operation period, CO2 flux conversed from “source” to “sink”. Compared with other reservoirs, CO2 flux was at a medium level among reservoirs all of the world and CH4 flux was at a medium-lower level.