The effects of the wetland plant Scirpus mariqueter on nitrous oxide (N2O) emissions in Yangtze estuary, China, were investigated using an in situ static chamber technique. Field measurements spanned the entire growing season (May to October) and encompassed a wide range of weather conditions typical of the subtropical monsoon climate of this region. Simultaneous measurement of carbon dioxide (CO2) and anatomical measurements were conducted to experimentally determine the gas transport mechanisms of S. mariqueter on N2O flux. S. mariqueter had a significant effect on N2O flux. Based on the comparison of light-dark and clipped-unclipped gas flux, N2O flux was negatively correlated with NEE (p < 0.0001) and NPP (p < 0.001) under light conditions when S. mariqueter was present but positively with temperatures in the dark condition or when S. mariqueter was clipped. Besides the plant uptake corresponding to the N2O negative flux in light chamber, it is reasonable to assume that because of the limitation of nitrate in sediment, coupled nitrification-denitrification is the main process of N2O producing. O2 transported into the S. mariqueter rhizosphere during photosynthesis stimulated denitrifier also would consume the N2O and would be induced to the N2O diffusing from atmosphere into sediment. Although photosynthetic activity of S. mariqueter attenuated N2O flux significantly over the course of the entire study period, creating a net sink for atmospheric N2O under light condition, the marsh of Chongming Island Dongtan wetland was a net source of atmospheric N2O during the active S. mariqueter growth phase (averaged flux was 98.3 μg N2O m−2 h−1).