Coastal salt marshes are sensitive to global climate change and may play an important role in mitigating global warming. To evaluate the impacts of Spartina alterniflora invasion on global warming potential (GWP) in Chinese coastal areas, we measured CH4 and N2O fluxes and soil organic carbon sequestration rates along a transect of coastal wetlands in Jiangsu province, China, including open water, bare tidal flat, and invasive S. alterniflora, native Suaeda salsa and Phragmites australis marshes. Annual CH4 emissions were estimated as 2.81, 4.16, 4.88, 10.79 and 16.98 kg CH4 ha−1 for open water, bare tidal flat, and P. australis, S. salsa and S. alterniflora marshes, respectively, indicating that S. alterniflora invasion increased CH4 emissions by 57–505%. In contrast, negative N2O fluxes were found to be significantly and negatively correlated (P < 0.001) with net ecosystem CO2 exchange during the growing season in S. alterniflora and P. australis marshes. Annual N2O emissions were 0.24, 0.38 and 0.56 kg N2O ha−1 in open water, bare tidal flat and S. salsa marsh, respectively, compared with −0.51 kg N2O ha−1 for S. alterniflora marsh and −0.25 kg N2O ha−1 for P. australis marsh. The carbon sequestration rate of S. alterniflora marsh amounted to 3.16 Mg C ha−1 yr−1 in the top 100 cm soil profile, a value that was 2.63- to 8.78-fold higher than in native plant marshes. The estimated GWP was 1.78, −0.60, −4.09 and −1.14 kg CO2eq ha−1 yr−1 in open water, bare tidal flat, P. australis marsh and S. salsa marsh, respectively, but dropped to −11.30 kg CO2eq ha−1 yr−1 in S. alterniflora marsh. Our results indicate that although S. alterniflora invasion stimulates CH4 emissions, it can efficiently mitigate increases in atmospheric CO2 and N2O along the coast of China.This article is protected by copyright. All rights reserved.