The carbon cycle is significantly affected by Spartina alterniflora invasion through its impact on blue carbon in many salt marshes. To determine the impacts on soil organic carbon (SOC), we studied the vertical and horizontal distribution of SOC. And stable carbon isotopes were used to explore the impact of the age of S. alterniflora invasion on SOC in Chongming Dongtan wetland located in the Yangtze River estuary, China. The results showed that the SOC concentration was higher in the S. alterniflora community than that in the native Phragmites australis community. The age of invasion and the SOC concentration increased with increasing elevation, while the SOC concentration decreased with increasing soil depth. The δ13C value became less negative at greater depth, which was related to the contribution from 13C- enriched carbon sources after 3 years of invasion. After 7 and 10 years, the δ13C value became more negative at greater depth in both communities. S. alterniflora had a positive effect on the soil carbon pool, and its contribution was related to soil depth. In the low tidal marshes, the contribution of S. alterniflora was negatively correlated with soil depth, while it was positively correlated with soil depth in the high tidal marshes. The results from this study will contribute to improved understanding of future ecological consequences.