Mangrove afforestation is considered an important measure in the “natural-based solution” for mitigating climate warming through sequestering massive carbon (C) into vegetation biomass, yet how the planted mangrove species facilitate soil C sequestration remains unclear. Here, we investigated the stock, source, and fraction of soil organic carbon (SOC) over 1 m depth after 20-year afforestation of five mangrove pure plantations (Acrostichum aureum, Acanthus ilicifolius, Aegiceras corniculatum, Kandelia obovate, and Excoecaria agallocha) on Qi’ao Island, South China. The results showed that SOC stocks did not significantly differ among the five plantations, with an average value of 16.7 kg C m⁻². Based on the two-end-member mixing model with plant–soil C stable isotope signatures, the autochthonous (mangrove-derived) C source accounted for 20.2–34.1% of SOC but varied significantly among the plantations. The SOC stock in particulate fraction (1.2–2.0 g C kg⁻¹) and mineral-associated fraction (14.3–16.0 g C kg⁻¹) also significantly differed among the plantations. The similar SOC stock but different source contributions and C fractions among the plantations observed here may have important implications for mangrove afforestation to optimize stand structure and maximize C sequestration.