In order to evaluate the effects of nitrogen deposition on CO2 and CH4 fluxes from a Cyperus malaccensis marsh in the Min River estuary at Daoqingzhou, Fujian, static chamber-gas chromatography (GC) techniques were used. CO2 and CH4 fluxes at a control (CK)[0 g·(m2·a)-1], N1[24 g·(m2·a)-1], N2[48 g·(m2·a)-1], and N3[96 g·(m2·a)-1] were measured and analyzed and the related environmental factors were recorded. The results show that,① compared to the control treatment, the effects of nitrogen deposition on the CO2 fluxes for N1 and N3 increased by 20.30% and 4.06%, respectively, whereas the CO2 fluxes for N2 reduced by 10.05%, furthermore, the CO2 fluxes under different treatments were not significantly different (P>0.05), except for the N2 and N3 treatments in December (P<0.05). ② Compared to the control treatment, the effects of nitrogen deposition on CH4 fluxes at N1, N2, and N3 were increased by 64.51%, 30.23%, and 80.57%, respectively, whereas the CH4 fluxes under different treatments were not significantly different (P>0.05). ③ There was significant positive correlation between CO2 and CH4 fluxes and soil temperature (P<0.05), however, the CO2 and CH4 fluxes were not significant with regards to soil pH and soil EC (P>0.05).