Mounting evidence supports that wetland ecosystems, one of the largest carbon pools on the earth, are exposed to ample nitrogen (N) additions due to atmospheric deposition or N loading from upstream agricultural fertilizer application. However, our understanding of how N enrichment affects the fluxes of greenhouse gases (GHGs) in wetlands is weak. A 5 year N addition experiment was conducted to examine the responses of CH4 and N2O fluxes as well as ecosystem respiration from wetlands in the Sanjiang Plain, Northeast China, through 2005 to 2009. Four levels of N addition (control, 0 kg N ha−1 yr−1; low-level, 60 kg N ha−1 yr−1; medium-level, 120 kg N ha−1 yr−1; high-level, 240 kg N ha−1 yr−1) were designed in this study. Overall, our results show that medium and high levels of N addition increased ecosystem respiration by 28% and 69% (P < 0.05), respectively, while low-level N addition has no effect on ecosystem respiration (P > 0.05). High-level N fertilization exerted stronger effects on ecosystem respiration in the initial year than the following years. It indicated that the effects of high-level N fertilization on CO2 might be overestimated by short-term observations. High-level N fertilization increased N2O emissions by 396% over the 5 years (P < 0.05), but the low- and medium-level-N addition did not exert any apparent effect on N2O emissions (P > 0.05). N2O emission under high-level N addition in the first and fifth years showed stronger pronounced responses to N addition compared with that from the third and fourth years, indicating the importance of long-term field observation. Over the 5 years, however, the low and medium-level N addition showed no effect on N2O emissions. The four levels of N addition exerted no effect on CH4 emissions (P > 0.05). Furthermore, the relationship between GHGs and soil temperature or water table depth varied among different plots and experimental time. Our findings highlighted the importance of gas species, experimental time, and the amount of fertilizer N with regard to the responses of GHG emissions to N fertilization.