Many studies have found that plant invasion can enhance soil organic carbon (SOC) pools, by increasing net primary production (NPP) and/or decreased soil respiration. While most studies have focused on C input, little attention has been paid to plant invasion effects on soil respiration, especially in wetland ecosystems. Our study examined the effects of Spartina alterniflora invasion on soil respiration and C dynamics in the Yangtze River estuary. The estuary was originally occupied by two native plant species: Phragmites australis in the high tide zone and Scirpus mariqueter in the low tide zone. Mean soil respiration rates were 185.8 and 142.3 mg CO2 m−2 h−1 in S. alterniflora and P. australis stands in the high tide zone, and 159.7 and 112.0 mg CO2 m−2 h−1 in S. alterniflora and S. mariqueter stands in the low tide zone, respectively. Aboveground NPP (ANPP), SOC, and microbial biomass were also significantly higher in the S. alterniflora stands than in the two native plant stands. S. alterniflora invasion did not significantly change soil inorganic carbon or pH. Our results indicated that enhanced ANPP by S. alterniflora exceeded invasion-induced C loss through soil respiration. This suggests that S. alterniflora invasion into the Yangtze River estuary could strengthen the net C sink of wetlands in the context of global climate change.