<p>Peatlands are vital for global carbon storage, but drainage significantly disrupts their natural carbon cycling. Drainage alters peatland soil environments in complex ways, affecting factors such as water table, soil temperature, organic carbon (SOC), pH, and microbial communities. However, how these factors interact to influence GHG emissions remains unclear. In this study, we compared water table, soil temperature, soil properties, microbial community structure, and GHG emissions across three zones of a peatland in Northeast China undergoing drainage: drained, transition, and natural areas. The average water table in the drained area was significantly lower than in the natural area (from 11.45&#xa0;cm to -13.47&#xa0;cm), shifting from waterlogged to unsaturated conditions. Deep soil temperatures in the drained area decreased by 1 ~ 3&#xa0;°C. The pH of the upper soil layer was higher in the drained area (5.05 ~ 5.29 vs. 4.64 ~ 4.71), while SOC was lower (197.31 ~ 374.75&#xa0;g/kg vs. 437.05 ~ 512.71&#xa0;g/kg). Aerobic bacteria (mainly <i>Solibacter</i>) were more abundant in the drained area, while methanogens (mainly hydrogenotrophic) declined significantly. Fungal diversity increased from the natural to drained area with increased negative interactions and enhanced network modularity. Drainage reduced CH₄ emissions but increased CO₂ and N₂O emissions, resulting in a significant rise in net GHG emissions (8.86 ~ 10.65 vs. 22.27 ~ 24.26 t CO₂-eq·ha⁻¹·season⁻¹), primarily driven by increased CO₂. CO₂ emissions were positively correlated with soil temperature, aerobic bacteria, facultatively anaerobic bacteria and pH, but negatively correlated with water table, anaerobic bacteria, soil moisture and C/N ratio. CH₄ flux was positively correlated with methanogens and water table, but negatively correlated with pH. The effects of drainage were more pronounced near drainage ditches, particularly for CO₂ emissions, highlighting the localized impacts of drainage on peatland GHG fluxes.</p>