As an important carbon pool around the world, wetlands play an important ecological carbon sink function in mitigating climate change. However, in the context of climate warming, carbon emissions (especially CH₄ emissions) are highly variable and uncertain. In order to explore the characteristics of carbon emission fluxes in Northeast saline-alkali wetlands under different water depth gradients, this study took the Momog Wetland as the study area. Five typical vegetation types (Phragmites australis, Bolboschoenus planiculmis, Schoenoplectus nipponicus, Typha orientalis C. Presl and Suaeda glauca) were selected to simulate habitats with different water depths through the Marsh Organ medium scale experimental ecosystem to reveal the changes of CH₄ and CO₂ emission fluxes and their environmental impact factors. The results showed that in water depth of -10 to 50 cm, the CH₄ emission fluxes of five selected vegetation species in the growing season ranged from 0.07 to 86.74 mg/(m²·h), with an average value of 8.89 mg/(m²·h). The main driving factors were water depth, air temperature and surface 10-cm soil moisture. In the water depth range of the study, the CO₂ emission flux of the vegetation growing season ranged from 10.59 to 1891.08 mg/(m²·h), and the average CO₂ emission flux was 450.12 mg/(m²·h). The main influencing factors were water depth, air temperature and surface 10-cm soil water content. Diverse vegetation had different contribution on carbon emission. Reed and cattails had the highest CH₄ emission, while Scirpus had the highest CO₂ emission. The carbon emission presented a segmented pattern with the water depth change. The CH₄ emission showed a trend of first increasing and then decreasing with the water depth change, while the CO₂ emission showed an opposite pattern, i.e., first decreasing and then increasing with the water depth change. The critical threshold of the water depth was 22 cm. In various water depth ranges, the sensitivity of CO₂ emissions to water depth was greater than that of CH₄. In case of the water depth ＞22 cm, both CH₄ and CO₂ show higher water depth sensitivity. When the water level was less than 22 cm, both CH₄ and CO₂ show higher temperature sensitivity. However, when the water level was greater than 22 cm, both of them were not sensitive to temperature. The results showed that under the background of warming, the key ecosystems in the water-land transition zone of typical saline-alkali wetlands in Northeast China typically show asymmetric response patterns in different water depth ranges, and frequent water level fluctuations will greatly change the wetland carbon emission pattern, thus affecting the stable play of wetland carbon function.