This study aimed to assess how sediment organic carbon (SOC) dynamics were affected by mangrove community structures. Sediment attributes and community structures of the Avicennia marina, Aegiceras corniculatum, Rhizophora stylosa, and Bruguiera gymnorrhiza communities were analyzed, based upon field investigation in Yingluo Bay of South China. Aboveground biomass (AGB), belowground biomass (BGB) and tree height obviously increased with the self-thinning process, while basal area significantly decreased. The self-thinning exponent was 1.382 for AGB and 1.254 for BGB, conforming to the 4/3 self-thinning rule. However, self-thinning exponent for basal area was only 0.4866. SOC content non-linearly increased with the increase of AGB, BGB, and tree height. Mangrove-derived carbon increased through in situ organic material inputs with mangrove growth. The negative correlation between tree density and SOC content was not in line with the previous studies for planted mangroves. SOC dynamics of natural mangroves may be partially different from planted mangroves.