The recovery of carbon stocks through the afforestation of degraded lands is a management practice that can be applied to mitigate rising concentrations of atmospheric carbon dioxide; however, due to economic pressure, most plantations are cut down in the growth stage, and the effect of forest stand age on soil carbon accumulation is unknown. We evaluated the effects of forest stand age on soil organic carbon (SOC), soil aggregate stability, and aggregate-associated SOC during afforestation. We collected soils along a chronosequence of 10, 20, 40, 60, and 100 years following restoration with P. massoniana after forest fires in the subtropical region of China. The results showed that the soil aggregates were primarily macroaggregates (>10 mm, 2–5 mm), and the stability of the soil aggregates first increased and then decreased as time progressed. The stability of the soil aggregates was at its maximum at 20 years post-planting. The mean weight diameter (MWD), geometric mean diameter (GMD) and fractal dimension (D) were 5.90 ± 0.17 mm, 4.25 ± 0.21 mm and 2.10 ± 0.04 mm, respectively, for the soil aggregates in the 0–20 cm layer. SOC content continuously increased with time since restoration, and SOC storage was mainly concentrated in the soil aggregates with sizes of >10 mm and 2–5 mm. Compared with the forests with restoration times of 10 years, the SOC storage in the 0–20 cm layer in the 20-, 40-, 60-, and 100-year-old forests increased by 10.10%, 9.57%, 31.39% and 69.40%, respectively. Compared with the forests with restoration times of 10 years, the SOC storage in the 80–100 cm layer of 20- and 40-year-old forests did not differ significantly, but those in the 60- and 100-year-old forests increased by 83.76% and 116.85%, respectively. For the forests between 10 and 100 years of age, the soil carbon sequestration rates were 0.33 ± 0.02 (0–20 cm), 0.42 ± 0.07 (20–40 cm), 0.39 ± 0.09 (40–60 cm), 0.33 ± 0.05 (60–80 cm) and 0.28 ± 0.03 (80–100 cm) Mg·C·ha−1·a−1. We concluded that SOC accumulation during afforestation occurs mainly in macroaggregates, which have faster turnover than microaggregates. The soils of mature and over-mature forests still have high carbon storage and sequestration rate, especially in the deeper soil layers (60–80 cm, 80–100 cm).