This study observes the characteristics and influencing factors of carbon fluxes of the Momoge salt marsh ecosystem over four years, which behaves as a CO2 sink. The daily, seasonal, and interannual variations of CO2 fluxes in the Momoge salt marshes were observed using the eddy covariance method and compared with various environmental factors. An overall daily “U” shaped distribution was observed, with uptake during the day (negative values) and release at night (positive values). Annually, the carbon fluxes in the study area roughly exhibit a “V” shape. Carbon fluxes during the non-growing season predominantly showed positive values, indicating the release of CO2 into the atmosphere. Photosynthetically active radiation was the primary influencing factor affecting hourly and daytime variations in net ecosystem exchange (NEE) during the growing season, while temperature was the main factor influencing nighttime NEE dynamics. Air temperature, soil temperature, photosynthetically active radiation, precipitation, and water level all had significant impacts on daily net CO2 exchange. At the monthly scale, larger values of soil temperature, air temperature, photosynthetically active radiation, and aboveground biomass correspond to a stronger carbon absorption capacity of the ecosystem. Overall, temperature remains the primary factor for carbon fluxes in the Momoge wetlands.