Since the impoundment in 2003, the flux of CO₂, CH₄ in the Three Gorges Reservoir (TGR) has changed significantly compared with the pre-impoundment status. Accessing the influence of the construction and operation of the TGR on these greenhouse gas fluxes has attracted much attention. In this paper, we reviewed the experience of monitoring and analysis of CO₂, CH₄ fluxes in TGR since 2009. At present, air-water diffusion was the major pathway for carbon emissions in the reservoir. Terrigenous organic carbon input was the main carbon source leading the production of CO₂ and CH₄ in the reservoir. Yet, the contribution of autochthonous organic carbon seemed to be with growing significant. Compared with pre-impoundment status, a net increase of greenhouse gas emissions in TGR is evident. Flooding accounted for about 20% of the net increase of the reservoir formation. Anthropogenic pollution in the reservoir region did not significantly to the net increase of CO₂ emissions. In addition, the dam acting as barriers and reservoir aquatic ecosystem reconstruction were major contributors for the net greenhouse gas emissions. Sampling campaigns and research in the past decade promoted the improvement and optimization of monitoring system of the greenhouse gas emissions in TGR. Application of new monitoring methods and technologies also provided support and reimbursement. However, the hydro-ecological mechanism driving the carbon cycle in the reservoir under complex hydrological environment is still unclear, which is a difficulty in the long-term trend prediction of the reservoir carbon flux. In the future, innovation of monitoring technology will be applied to promote the accurate calculation of the carbon flux of TGR. It is still urgent to put forward more scientific and effective models or methods to support the long-term trend prediction and serve the reservoir carbon management.