With the LGR-floating chamber method, a 24-hour continuous monitoring was carried out in the initial impoundment period of Three Gorges Reservoir, in order to understand the greenhouse gases fluxes (carbon dioxide and methane) across the water-air interface of Caotang River which is the primary tributary of the reservoir. The results indicated that the fluxes of carbon dioxide and methane across the water-air interface appeared an obvious characteristic of diurnal variation. The fluxes of carbon dioxide ranged from -81.642 to 180.991 mg/(m²·h), and the average fluxes of carbon dioxide were 17.346 mg/(m²·h). As a result, the overall carbon dioxide showed “absorb by day and emit at night”. Methane was emitted all day with the average fluxes of methane 0.064 mg/(m²·h) showed “strong at day and weak at night”. The fluxes of carbon dioxide and methane had a positive correlation with wind speed while a negative correlation was observed with water temperature of surface layer, dissolve oxygen and chlorophyll-a. It could be explain the most important factors that influence emissions at water-air interface were phytoplankton photosynthesis and bacterial metabolism process in the surface water. The changes in greenhouse gases emissions at water-air interface were also relevant to special environment (density current and thermal stratification) due to the interaction between main current and tributaries. The hydrodynamic factors were the key factors that affect carbon cycle and the greenhouse gases fluxes across the water-air interface in backwaters of tributaries, which would be worth researching.