As important intermediates in the process of carbon cycle in estuarine wetlands,methane (CH_4) is the important greenhouse gas that only seconds to carbon dioxide (CO_2) in the atmosphere. Accurate estimation of CH_4 emission inventory is important in predicting the global warming tendency. The static closed chamber-chromatograph method was used to investigate the monthly CH_4 fluxes from February 2011 to December 2012 in the salt marshes of Yangtze River estuary. The results indicated that salt marshes in Yangtze River estuary acted as a net source of atmospheric CH_4 and the annual average CH_4 fluxes was 1. 00 mg·m~(-2)·h~(-1) in 2011 when the Scirpus mariqueter was the dominant species. After the full-scale invasion of the alien Spartina alterniflora,biomass of Scirpus mariqueter decreased greatly in 2012,with the annual average CH_4 fluxes decreased to 0. 55 mg·m~(-2)·h~(-1). According to Pearson correlation analysis,sediment organic carbon,solar radiation and the water content were not the main factors of CH_4 fluxes. In addition,CH_4 fluxes were significantly positively correlated with both aboveground biomass of Scirpus mariqueter(p=0. 001,r=0. 928) and temperature (p<0. 01,r=0. 432) in 2011. Along with the invasion of Spartina alterniflora in 2012,CH_4 fluxes reached the highest value in May. The total CH_4 emissions also decreased significantly due to the invasion of Spartina alterniflora in 2012.