The fast growing exotic Sonneratia apetala has been widely used to increase the mangrove area in China. Despite of the rapidly accumulated biomass, S. apetala does not increase the soil organic carbon (SOC) storage comparing with native mangroves. The belowground biomass of mangrove, especially its fine roots, plays an important role in SOC sequestration. Here, the soil physicochemical properties, vegetation and fine-root biomass and SOC stock were compared between S. apetala (22-year-old) plantation and native mangrove at different stages (20, 40, and 80-year-old) The 22-year-old S. apetala already had a higher vegetation biomass and fine root biomass than the 20-year-old and 40-year-old native mangrove. However, no significant differences in the SOC stock were observed between S. apetala and native mangrove (20-year-old and 40-year-old). The biomass of vegetation and fine root and SOC stock of S. apetala were all significantly lower than that of 80-year-old Rhizophora stylosa. Multiple stepwise regression analysis suggested that lower C:N ratio of fine roots and soil salinity in S. apetala can promote the decomposition rate of fine roots and then offset the carbon accumulation advantage related to higher fine root biomass. Restoration of mangrove was effective to enhance soil carbon stock, but the exotic S. apetala should be decreased or avoided in the future, especially in the Natural Reserve.