Wetlands are the largest natural sources of atmospheric methane (CH4) and are often susceptible to plant invasion and hydrological fluctuations. However, the effect of plant invasion on wetland CH4 emissions is still controversial, and little is known about the variation of invasion-induced CH4 emissions under heterogeneous conditions. A pairwise experimental design between Spartina alterniflora (invasive plant) and Phragmites australis (native plant) stands in high elevation sites (H-sites) and S. alterniflora and Scirpus mariqueter (native plant) stands in low elevation sites (L-sites) of the Yangtze River estuary was used to investigate how plant invasions affect CH4 emissions and whether CH4 emission changes significantly differ between the H- and L-sites with heterogeneous conditions. A static closed chamber method was used to conduct gas sampling measurements at both H- and L-sites. In addition, plant biomass and soil properties were investigated in both invasive and native plant stands. CH4 emissions from the S. alterniflora stands were all significantly higher than those from the native plant stands at both H- and L-sites. Furthermore, the difference in CH4 emissions between S. alterniflora and P. australis stands in the H-sites was significantly lower than that between S. alterniflora and S. mariqueter stands in the L-sites. Plant biomass, soil organic carbon, and microbial biomass in S. alterniflora stands were all significantly higher than those in the native plant stands in both H-sites and L-sites. The soil properties also changed. Our results indicate that the S. alterniflora invasion significantly enhanced CH4 emissions from wetlands in the Yangtze River estuary. The invasion-related CH4 emissions were highly spatially variable; this variability may have been driven by the soil’s anaerobic environments, induced by hydrological dynamics. These results can have important implications for improving our ability to predict invasion-induced changes in CH4 emissions from wetlands in the context of global climate change.