Estuaries, considered as the important carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) sources to the atmosphere, are increasingly affected by near-bottom hypoxia. However, the impact of estuarine hypoxic zone development on GHGs production and discharge remains poorly understood due to the seasonal and spatially distributed heterogeneity of estuarine hypoxia occurrence and the lack of simultaneous monitoring of the distribution of bottom hypoxic waters and the vertical distribution of GHGs. Here, we conducted high spatial resolution vertical stratification sampling and analysis of water column GHGs in the Pearl River Estuary (PRE), a large estuary with frequent hypoxia in recent years. Our results showed that Pearl River runoff is the main source of GHGs in the PRE. Strong nitrification is an important N2O production mechanism in the PRE. In situ generation of water and resuspension of surface sediments were the main sources of CH4 in bottom water, while massive organic matter (OM) mineralization is the main driver of CO2 in bottom water. The development of a hypoxic zone in the PRE significantly increased the concentration of N2O and CH4 in the bottom water and thus increased air-water fluxes. The air-water fluxes of N2O, CH4 and CO2 of PRE in summer were 31.9 ± 7.5 μmol m−2 d−1, 192.5 ± 229.4 μmol m−2 d−1 and 51.9 ± 14.1 mmol m−2 d−1, respectively. This study reveals that GHGs fluxes from estuarine waters to the atmosphere will increase significantly with increasing eutrophication caused by human activities and the expansion of hypoxic zones in estuarine waters.