As an important soil carbon pool in Qinghai-Tibet Plateau (QTP), alpine peatland are extremely sensitive to global change. Duration of drainage and water table drawdown lead to rapid soil degradation and C losses, and this may worsen under warming as the soils are no longer protected by anaerobic conditions. Hence, the objective of this study was to assess the effect of drainage on microbial characteristics, greenhouse gas (GHG) emissions and their influencing factors, and further analyze whether the the variability of GHG emissions increases with warming. The results showed that the influence of water table drawdown on microbial community structure was greater than that of duration of drainage. Both the fungal and prokaryotic community compositions varied with water table gradient, and soil microbiota may served as a biomarker to analyze the differences in GHG emissions among three different water table treatments. Intriguingly, the GHG emission decreased with the increase of drainage age, while water table drawdown reduced the CO2 and CH4 emission rates, and increased N2O emission rates. In addition, high temperature increased CO2 by 75% and N2O by 42%, but not significantly decreased the CH4 emission rates. Structural equation modeling suggested that microbial community composition was the primary factor affecting GHG emissions from drained peatlands, especially prokaryotes. Overall, our results indicate that water table plays a more important role in GHG emissions than duration of drainage, and the variability of GHG emissions increases with warming.