Drainage and cultivation have turned peatlands from carbon (C) sinks into hotspots for greenhouse gas (GHG) emissions. Raising the water table and planting of winter cover crops are potential strategies to help reduce peat oxidation and re-initiate net C accumulation during the non-cropping period. However, the effects of these practices as well as their interactions on GHG emissions remain unclear. Here, we carried out an outdoor mesocosm experiment to elucidate the effect of water table levels (−30 cm and −50 cm) and winter cover crop cultivation (vetch, rye, no plant) on carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) fluxes during the winter period (November-April). Soil-atmosphere GHG exchange, GHG concentrations within the peat profile and soil water solute concentrations were monitored. Our results showed that high water table significantly reduced ecosystem respiration, while it had no net effect on N2O and CH4 fluxes. Uptake of available N by the cover crop significantly reduced nitrate in soil solution, thereby lowering the potential for leaching and both direct and indirect N2O emissions. No interactive effects between water table levels and cover crops were detected for any of the measured GHG fluxes. Seasonal variations of GHG fluxes were positively correlated with soil air concentrations at −15 cm and −40 cm depths, which were further regulated by dissolved organic C, nitrate concentration, and anaerobic conditions in the soil. This study suggests that there is great potential to raise water table levels and introduce green cover crops to reduce GHG emissions. Further studies are needed to achieve a complete evaluation of these strategies outside of the growing season, which may provide a significant mitigation benefit in C-rich cultivated peatlands.