Abstract: Zhuyi River, Caotang River, two tributaries of Three Gorges Reservoir (TGR), and its adjacent mainstream were selected as survey area. In the spring algal bloom period, the airwater interface greenhouse gas fluxes in relation to environmental factors were observed in March, 2015. The results showed that during this period, the mainstream of TGR was a source of CO₂ and its flux was 85.01 mmol·m^-2·d^-1. Zhuyi River, slightly influenced by the mainstream, was a sink of CO₂, and its flux ranged from  -73.26 to -30.38 mmol·m^-2·d^-1. However, Caotang River, intensely influenced by the mainstream, was a weak source of CO₂, and its flux ranged from 81.43 to 136.72 mmol·m^-2·d^-1. Correlation analysis showed that the CO₂ fluxes of different areas in TGR had a significant correlation with primary productivity of plankton. Influenced by the TGR operation, the difference of water regimes in different water areas in mainstream and tributaries resulted in spatial difference of biomass of plankton and intensity of carbon conversion and utilization, which would be the main factor for the high heterogeneity in the source or sink for airwater interfaces CO₂ in TGR.