To understand the influence of nitrogen fertilization on the carbon balance in the freshwater marshes, we measured the CO2 and CH4 emissions as well as net ecosystem exchange (NEE) of CO2 using the static chamber and gas chromatogram technique in situ over Deyeuxia angustifolia wetland in Sanjiang Plain. Results from the field observed indicated that fertilization increased the biomass and gross primary productivity (GPP) as well as the CO2 and CH4 emissions, while decreased the net ecosystem exchange of CO2 but not change the seasonal dynamics of CO2 and CH4 emissions as well as the NEE. Seasonal amount of CO2 and CH4 emission from the fertilization was respectively 34% and 145 % higher than that from the control, while the NEE and net carbon exchange decreased 70% and 81.6% due to the nitrogen fertilization. During the whole growing season of 2004 the ecosystem still showed the net uptake of the carbon not only in the fertilization treatment but also control. Thus, it can be assumed that nitrogen fertilization decreased the net carbon uptake from the atmosphere but not changed the ecosystem from a carbon sink to a source.