The objective of this study is to better understand the CO₂ emission flux characteristics in different microtopographic marshes of the Zoigê Plateau. The temporal and spatial variability of CO₂ emission flux in five sampling sites among three marshes were measured by the dark static chamber method and Fast Greenhouse Gas Analyzer during the growing seasons in 2013 and 2014. The three typical marshes were the permanently flooded zone, the seasonally flooded zone, and the transition zone between them. The results showed that the seasonal CO₂ emission fluxes of the permanently flooded hummock zone (PHK) and hollow zone (PHW) in the Zoigê Plateau marsh ranged from 38.99 to 1731.74 mg m^-2 h^-1 and 46.69 to 335.22 mg m^-2 h^-1, respectively. In addition, the seasonal CO₂ emission fluxes of the seasonally flooded hummock zone (SHK) and hollow zone (SHW) in the Zoigê Plateau marsh varied from 193.90 to 2575.60 mg m^-2 h^-1 and 49.93 to 1467.45 mg m^-2 h^-1, respectively. The non-flooded zone (Lawn) was located in the transition zone. The seasonal CO₂ emission flux in the Lawn changed from 194.20 to 898.75 mg m^-2 h^-1. During the growing seasons, the mean CO₂ emission fluxes in the PHW, PHK, Lawn, SHW and SHK zones in the Zoigê Plateau marsh were 143.73, 443.55, 522.86, 552.60, and 946.95 mg m^-2 h^-1, respectively. In general, the peak value of the CO₂ emission flux in the Zoigê Plateau marsh was achieved between July and August, while the low value of the CO₂ emission flux occurred in the early Spring and/or late Autumn. The results indicated that there was a significant and positive correlation between the seasonal CO₂ emission flux and soil temperatures at the 5-45 cm depth in the PHK, PHW, and SHK zones in the Zoigê Plateau marsh. Meanwhile, the seasonal CO₂ emission flux was also positively correlated with the soil temperature at 5 and 15 cm depth in the Lawn zone in the Zoigê Plateau marsh. Besides, the seasonal CO₂ emission flux in the SHW zone in the Zoigê Plateau marsh was positively correlated with the soil temperature at 5-30 cm depth. Additionally, the seasonal CO₂ emission flux was negatively correlated with water table depth in the PHW, SHW, SHK, and Lawn zones, while not correlated with water table depth in the PHK. Overall, about 87% of the seasonal variation of CO₂ emission flux could be explained by the changes of soil temperature (5 cm depth) and water table depth (CO₂ emission flux=56.479 T₅-11.170 WT-156.617, R²=0.874, P<0.001). Our results revealed that the CO₂ emission flux in five sampling sites among three marshes in the Zoigê Plateau exhibited an obvious spatial variability. The spatial variability of the CO₂ emission flux in the Zoigê Plateau marsh was mainly controlled by water table depth, and could be affected by the type of plant. In addition, the results also exhibited that the mean CO₂ emission flux was negatively correlated with the mean water table depth.