To investigate the effect of Spartina alterniflora invasion on soil organic carbon fractions and the stability of soil, the soil samples were collected from wetlands of mangroves and invasive species S. alterniflora (before invasion was mangrove forest) in the Zhangjiangkou Estuary, Jiulong River Estuary and Min River Estuary of Fujian, and Yueqing Bay of Zhejiang. The contents of soil organic carbon (SOC), soil organic carbon storage (SOCS), active organic carbon fractions (microbial biomass carbon-MBC, easily oxidized organic carbon-EOC and water soluble organic carbon-WSOC) and chemical bonded organic carbon components (calcium bonded organic carbon (Ca—SOC) and iron-aluminum bonded organic carbon (Fe (Al)—SOC)) were measured in laboratory. These results showed that compared with the mangrove, soil SOC, SOCS, MBC and EOC contents decreased after S. alterniflora invasion, especially SOC and SOCS, their reduction rates were about 9.86%～27.13% and 13.95%～26.29%, respectively. While, soil WSOC content had increased by 5.75%～53.52%. Soil chemical bonded organic carbon components were also influenced by S. alterniflora invasion. The ratio of Ca—SOC/SOC increased, while the ratio of [Fe (Al)—SOC+residual state SOC]/SOC decreased. These results indicated that S. alterniflora invasion not only changed the soil organic carbon pool, but also changed its stability. The chemical bond of soil organic carbon might be the main protective mechanism for the soil organic carbon stability in mangrove wetland, which was important for mangrove carbon sink function.