There is a wide concern on the greenhouse gases emission due to dam construction in recent years. However, diel variation of reservoir greenhouse gases fluxes was seldom reported. To track the diel dynamics of greenhouse gases fluxes in the backwater area of the Pengxi River, Three Gorges Reservoir and elucidate the controlling factors of the fluxes, four 24-h monitoring-campaigns in Aug., Nov. of 2010 and Feb., May of 2011 were carried out in a whole reservoir operation year in Lake Gaoyang. We found that the daily total emission of CO₂ were -8.34, 73.94, 28.13 and -20.12 mmol/(m²·d) in the above periods, respectively. While the fluxes of CH₄ during these 4 monitoring campaigns were 2.22, 0.11, 0.32 and 7.16 mmol/(m²·d), respectively. The diel varied among the campaigns. The emission of CO₂ and CH₄ were showed to have different pathways for their asynchronous fluxes during the study. A correlation analysis revealed that photosynthesis and respiration in water column was a key controlling process for CO₂ fluxes in this area. Furthermore, instantaneous meteorological parameters, i. e. wind speed, water-air temperature differences, were also significant factors that impact the fluxes of CO₂ in high water level operation period of the reservoir. However, the variations of CH₄ might be regulated by water temperature changes.