Turbulent mixing is enhanced in shallow lakes. As a result, exchanges across the air-water and sediment-water interfaces are increased, causing these systems to be large sources of greenhouse gases. This study investigated the effects of turbulence on carbon dioxide (CO2) and methane (CH4) emissions in shallow lakes using simulated mesocosm experiments. Results demonstrated that turbulence increased CO2 emissions, while simultaneously decreasing CH4 emissions by altering microbial processes. Under turbulent conditions, a greater fraction of organic carbon was recycled as CO2 instead of CH4, potentially reducing the net global warming effect because of the lower global warming potential of CO2 relative to CH4. The CH4/CO2 flux ratio was approximately 0.006 under turbulent conditions, but reached 0.078 in the control. The real-time quantitative PCR analysis indicated that methanogen abundance decreased and methanotroph abundance increased under turbulent conditions, inhibiting CH4 production and favoring the oxidation of CH4 to CO2. These findings suggest that turbulence may play an important role in the global carbon cycle by limiting CH4 emissions, thereby reducing the net global warming effect of shallow lakes.