Invasive Spartina alterniflora accumulates organic carbon rapidly and can utilize a wide range of potential precursors for dimethyl sulfide (DMS) production, as well as a wide variety of methanogenic substrates. Therefore, we predicted that S. alterniflora invasion would alter the relationships between DMS and methane (CH4) fluxes along the interacting gradients of tidal influence and vegetation, as well as the ecosystem-atmosphere exchange of DMS and CH4. In this study, we used static flux chambers to measure DMS and CH4 fluxes in August (growing season) and December (non-growing season) of 2013, along creek and vegetation transects in an Eastern Chinese coastal salt marsh. S. alterniflora invasion dramatically increased DMS and CH4 emission rates by 3.8–513.0 and 2.0–127.1 times the emission rates within non-vegetated regions and regions populated with native species, respectively, and significantly altered the spatial distribution of DMS and CH4 emissions. We also observed a substantial amount of variation in the DMS and CH4 fluxes along the elevation gradient in the salt marsh studied. A significant relationship between DMS and CH4 fluxes was observed, with the CH4 flux passively related to the DMS flux. The correlation between CH4 and DMS emissions along the vegetation transects was more significant than along the tidal creek. In the S. alterniflora salt marsh, the relationship between DMS and CH4 fluxes was more significant than within any other salt marsh. Additionally, CH4 emissions within the S. alterniflora salt marsh were more sensitive to the variation in DMS emissions than within any other vegetation zone. The spatial variability in the relationship observed between DMS and CH4 fluxes appears to be at least partly due to the alteration of substrates involved in DMS and CH4 by S. alterniflora invasion. In the S. alterniflora salt marsh, methanogenesis was more likely to be derived from non-competitive substrates than competitive substrates, but within the creek and other vegetation zones, methanogenesis was inhibited by sulfate reduction. This suggests that methanogenesis and sulfate reduction were spatially isolated within the coastal salt marsh. Therefore, we conclude that the invasive S. alterniflora altered the ecosystem-atmosphere exchange of DMS and CH4 and the responses of the relationship between these two gases to interacting gradients of tidal inundation and vegetation within an Eastern Chinese coastal salt marsh.