There has been limited research on the effect of eucalyptus harvest residue management on soil organic carbon (SOC) in subtropical environments. This research evaluated the effect on soil C indices of the following eucalyptus harvest residue managements: AR, with all forest remnants left on the soil; NB, where bark was removed; NBr, in which branches were removed; NR, which removed all residues; and NRs, which is same as NR but also used a shade net to prevent the litter from the new plantation from reaching the soil surface. C stocks within the soil depths of 0–20 cm and 0–100 cm increased linearly with the C input from eucalyptus harvest residues. In the layer of 0–20 cm, the lowest soil C retention rate was 0.23 Mg ha−1 year−1, in the NR treatment, while in the AR treatment, the retention rate was 0.68 Mg ha−1 year−1. In the 0–100 cm layer, the highest C retention rate was obtained in the AR (1.47 Mg ha−1 year−1). The residues showed a high humification coefficient (k1 = 0.23) and a high soil organic matter decomposition rate (k2 = 0.10). The carbon management index showed a close relationship with the C input and tree diameter at breast height.