Carbon stock is an important indicator of cumulative ecosystem productivity. Using this indicator, and based on field sampling data, this paper compared the long-term difference in carbon stocks between aerial seeding (AS) and natural regeneration (NR) forests of Pinus massoniana in sub-tropic forests, China, in order to assess the effectiveness of AS in a highly degraded forest landscape. The results showed that the carbon stocks of stems, branches, roots, and trees (including stems, branches, leaves, and roots) were 140%, 85%, 110%, and 110%, significantly higher (p < 0.05) in the NR forests than those in the AS forests at the ages of 11–20 years, respectively. In addition, the carbon stocks of understory, litter and soil were also 176%, 151%, and 77%, significantly higher (p < 0.05) in the NR forests than those in the AS forests at the same age range, respectively. However, with increasing age (i.e., >21 years), those differences became statistically insignificant (p > 0.05). The total carbon stocks of the two forest types also showed a similar pattern. Those results clearly demonstrate that AS was an effective mean for restoring carbon stocks in highly degraded areas, even though their early growth was lower than the NR forests, and thus can be applied in the regions where the areas with limited seed sources and road accessibility.