Background and Objectives: The rapid spread of invasive Spartina alterniflora Loisel. in the mangrove ecosystems of China was reduced using Sonneratia apetala Buch.-Ham. as an ecological replacement. Here, we studied the effects of invasion and ecological replacement using S. apetala on soil organic carbon fractions and stock on Qi’ao Island. Materials and Methods: Seven sites, including unvegetated mudflat and S. alterniflora, rehabilitated mangroves with different ages (one, six, and 10 years) and mature native Kandelia obovata Sheue, Liu, and Yong areas were selected in this study. Samples in the top 50 cm of soil were collected and then different fractions of organic carbon, including the total organic carbon (TOC), particulate organic carbon (POC), soil water dissolved carbon (DOC) and microbial biomass carbon (MBC), and the total carbon stock were measured and calculated. Results: The growth of S. alterniflora and mangroves significantly increased the soil TOC, POC, and MBC levels when compared to the mudflat. S. alterniflora had the highest soil DOC contents at 0–10 cm and 20–30 cm and the one-year restored mangroves had the highest MBC content. S. alterniflora and mangroves both had higher soil total carbon pools than the mudflat. Conclusions: The invasive S. alterniflora and young S. apetala forests had significantly lower soil TOC and POC contents and total organic carbon than the mature K. obovata on Qi’ao Island. These results indicate that ecological replacement methods can enhance long term carbon storage in Spartina-invaded ecosystems and native mangrove species are recommended.