Forest fragmentation threatens the ecosystem carbon (C) storage. The distribution patterns of ecosystem C density are poorly documented for fragmented forests of differing patch size. The objectives of this study were to examine C density in these forest ecosystems and the influence of edge effects on C density. Allometric equations were used to quantify aboveground biomass. Carbon density was estimated by analyzing the C concentration of each component. We found that ecosystem carbon density ranged from 173.9 Mg ha(-1) in the small sized forest fragments, to 341.1 Mg ha(-1) in the contiguous evergreen sub-tropical forest. Trees (46.5%) and mineral soil (50.2%) were the two largest contributors to the total ecosystem C pool in all fragments. Both C and nitrogen (N) in soil and fine roots were highly heterogeneous among the different fragment sizes and soil depths. We concluded that ecosystem C density of forest fragments were significantly influenced by patch size and edge effects. The fragmented forests in southern China play an important role in the C budget, and need urgent conservation. These results are likely to be further integrated into forest management plans and generalized into other contexts, to evaluate C stocks at the landscape scale.