Abstract: Estimation on annual greenhouse gas fluxes in reservoirs is crucial for the assessment of reservoir greenhouse gas effects. A 1a research was conducted in Pengxi River backwater area, Three Gorges Reservoir to estimate annual water-air CO₂ and CH₄ fluxes. Taken the 24h continuous monitoring data in Gaoyang Lake as reference, 2 methods, i.e. underwater topographical method and environmental controlling factor method, were carried out to estimate the annual fluxes based on monthly field data. The field sampling results showed that mean value of the CO₂ fluxes among the sampling spot was (3.05±0.46) mmol/(m²· h), while that of CH₄ was (0.050 1±0.009 6) mmol/(m²·h). The annual estimation of CO₂ and CH₄ fluxes in the Pengxi River backwater area based on underwater topographical method was 40 060.5 t and 540.9 t respectively. With the environmental controlling factor method, the annual estimation of CO₂ and CH₄ fluxes was 39 073.0 t and 467.2 t respectively. Taken the annual estimation result from environmental controlling factor method as reference, the weighted average CO₂ fluxes during the study was 43.26 mmol/(m²·d), while that of CH₄ was 1.42 mmol/(m²·d). Generally, both of the CO₂ and CH₄ weight average fluxes were shown to be in the mid-range in the global data sets, although that of CO₂ was showed in slightly higher bound.