Nitrogen (N) deposition has increased in recent years and is significantly affected by global change and human activities. Wetlands are atmospheric CH4 and N2O sources and may be affected by changes in N deposition. To reveal the effects of increased N deposition on peatland greenhouse gas exchange, we observed the CH4 and N2O emissions from controlled microcosms collected from a temperate peatland in the Xiaoxing’an mountains, Northeast China. We found that the moss biomass did not change, but the total herb biomass increased by 94% and 181% with 5 and 10-times-higher N deposition, respectively. However, there were no significant changes in CH4 emissions from the microcosms with N addition. The unchanged CH4 emissions were mainly caused by the opposite effect of increased nitrate and ammonium concentrations on soil CH4 production and the increased plant biomass on CH4 emission. We also found that the manipulated microcosms with 5 and 10-times-higher N deposition had 8 and 20-times-higher seasonal average N2O emissions than the control microcosms, respectively. The increased N2O emissions were mainly caused by short-term (≤7 d) pulse emissions after N addition. The pulse N2O emission peaks were up to 1879.7 and 3836.5 μg m−2 h−1 from the microcosms with 5 and 10-times-higher N deposition, respectively. Nitrate and ammonium concentrations increasing in the soil pore water were the reason for the N2O emissions enhanced by N addition. Our results indicate that the increase in N deposition had no effects on the CH4 emissions but increased the N2O emissions of the temperate peatland. Moreover, pulse emissions are very important for evaluating the effect of N addition on N2O emissions.