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 accelerate peatland degradation due to the soil changed from anaerobic condition to aerobic condition, which may even worsen under climate warming. Hence, the objective of our research was to evaluate 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 communities were 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 decreased the emissions of CO2 and CH4, and increased the emission of N2O. In addition, high temperature increased CO2 by 75% and N2O by 42%, but not significantly decreased the CH4 emission rates. Structural equation modeling showed that microbe was the primary factor affecting GHG emissions from drained peatlands, especially prokaryotes. In all, this study indicate water table has a greater effect on GHG emissions than duration of drainage, and the variability of GHG emissions increases with warming.