Mangrove forests are large pools of soil organic carbon (SOC) found across the world, and play a vital role in global carbon (C) cycling. In this study, to investigate the effects of spatial factors on SOC in mangrove forests, soil samples at different depth layers from upper estuary (UE), lower estuary (LE), and tidal inlet (TI) in the Qinglangang mangrove forest in Southern China were collected and the differences in SOC among the layers and geomorphological settings were compared. The mean SOC content showed a pattern of LE (4.63 ± 1.28%) > UE (2.94 ± 0.73%) > TI (1.44 ± 0.33%). SOC content and storage decreased with soil depth in TI, but increased in UE. The total SOC storages (0–80 cm) of sites TU, UE, and LE, were 104.41 ± 16.63, 207.14 ± 44.83, and 228.78 ± 19.37 Mg/ha, respectively. The results suggested that top- and subsoil organic C content and storage were largely dependent on their specific location, which underwent different river-sea interactions and human activities. The SOC of the soil profile varied at different sites, implying that the current C storage of mangrove ecosystems can be accurately estimated by quantifying the C of sediments at sites.