Up to now, there have been few studies in the annual fluxes of greenhouse gases in lakes of subtropical regions. The fluxes of methane (CH4) and carbon dioxide (CO2) across air–water interface were measured in a shallow, hypereutrophic, subtropical Lake Donghu (China) over a year cycle, using a static chamber technique. During the year, Lake Donghu emitted CH4 and CO2; the average flux of CH4 and CO2 was 23.3±18.6 and 332.3±160.1mgm−2 d−1, respectively. The fluxes of CH4 and CO2 showed strong seasonal dynamics: CH4 emission rate was highest in summer, remaining low in other seasons, whereas CO2 was adsorbed from the atmosphere in spring and summer, but exhibited a large emission in winter. Annual carbon (C) budget across air–water interface in Lake Donghu was estimated to be 7.52±4.07×108 g. CH4 emission was correlated positively with net primary production (NPP) and temperature, whereas CO2 flux correlated negatively with NPP and temperature; however, there were no significant relationships between the fluxes of CH4 and CO2 and dissolved organic carbon, a significant difference from boreal lakes, indicating that phytoplankton rather than allochthonous matter regulated C dynamics across air–water interface of subtropical lake enriched nutrient content.