Afforestation is an important strategy to promote vegetation restoration of degraded karst ecosystems while enhancing terrestrial carbon sequestration. To date, the effects of afforestation on soil carbon and nitrogen fractions and their biochemical stability in the karst-cluster depression region are poorly understood. In this study, 14 sets of surface (0~15 cm) and sub-surface (30~45 cm) soil samples were collected from the maize field and its neighbouring plantation forests in the karst-cluster depression region of Guangxi, and the soil carbon and nitrogen fractions (labile carbon and nitrogen in pool I, labile carbon and nitrogen in pool II, and carbon and nitrogen in the non-lable pool) were determined using the acid hydrolysis method. The study showed that the contents of total organic carbon, total nitrogen, labile carbon and nitrogen pools, non-labile carbon and nitrogen pools in both surface and subsurface soils were significantly increased after 20 years of afforestation. The soil carbon pool activity (labile carbon pool/ non-lable carbon pool) was significantly lower, but the carbon pool stability (non-labile carbon as a proportion of total soil organic carbon) was significantly higher in the plantation forest than in the maize field. Stepwise regression analyses showed that fine root biomass, calcium carbonate and exchangeable calcium ions were the main factors responsible for the increase of soil organic carbon, nitrogen and their fractions following afforestation.