The CO_2 and CH_4 emission fluxes in the Zoige Plateau Marsh were monitored by using the dark static chamber and Fast Greenhouse Gas Analyzer at three typical sampling sites (natural marsh, drainage marshes in the 1990s and 1970s) from May to October in 2014. The results showed that the drainage increased the soil temperature (5, 20 and 45cm depth) and reduced the water level. The ecosystem CO_2 emission fluxes of the drained marshes in 1990s [(680329) mg CO_2/(m~2 ·h)] and 1970s [(973234) mg CO_2/(m~2 ·h)] were 200% and 330% higher than that in the natural marsh. While, the ecosystem CH_4 emission fluxes of the drained marshes in 1990s [(0.780.52) mg CH_4/(m~2 ·h)] and 1970s [(-0.010.02) mg CH_4/(m~2 ·h)] were 90% and 100% lower than that in the natural marsh, respectively. Taking into consideration of both CO_2 and CH_4 emission fluxes, the ecosystem carbon (C) emission fluxes of the drained marshes in 1990s [(18689) mg C/(m~2 ·h)] and 1970s [(26564) mg C/(m~2 ·h)] were 180% and 300% higher than that in the natural marsh. Besides, there was a significant positive correlation between the ecosystem CO_2 emission fluxes and the soil temperature of 5cm depth in the three typical sampling sites. Whereas, there was an obvious negative correlation between the ecosystem CO_2 emission flux and the water level in the 1990s drained marsh. In addition, the ecosystem CH_4 emission flux in the natural marsh was notably positively correlated with the soil temperatures at 5, 20 and 45cm depth. However, the ecosystem CH_4 emission flux in the 1970s drained marsh was remarkably negatively correlated with the soil temperatures at 20 and 45cm depth. Meanwhile, we also found that there was a significant positive relation between the ecosystem CH_4 emission flux in the 1990s drained marsh and the water level. This research suggested that the marsh drainage could significantly increase the ecosystem C emission flux from the soil into the atmosphere in the Zoige Plateau Marsh, subsequently decrease the soil C sink function, and further enhance the regional climate warming.