Evaluating soil organic carbon (SOC) and soil total nitrogen (STN) concentrations together with carbon and nitrogen stable isotope signatures across aggregate fractions can provide novel insights into the mechanisms underlying SOC and STN sequestration following afforestation. However, the impacts of different afforestation strategies on the distribution, transformation, and stabilization of SOC and STN among aggregate fractions, especially in degraded karst ecosystems, remain unclear. Here, aggregate size composition, SOC and STN concentrations, as well as delta C-13 and delta N-15 values in bulk soils and aggregate fractions were examined after 10 years of afforestation in a karst rocky desertification region. Eight treatments were selected, including five monoculture plantations (Pinus massoniana, Photinia glomerata, Pistacia weinmannifolia, Eucalyptus, and Fraxinus malacophylla), one mixed-species plantation dominated by F. malacophylla, P. massoniana, Rhus chinensis, Solanum deflexicarpum, and Campylotropis harmsii, as well as adjacent abandoned land and secondary forest as controls. Afforestation significantly increased SOC and STN storages relative to abandoned land, with larger gains under mixed-species afforestation (4.30 kg C m(-2) and 0.29 kg N m(-2)) than under monocultures (1.09-2.47 kg C m(-2) and 0.08-0.16 kg N m(-2)). Meanwhile, mixed-species afforestation significantly increased the >2 mm aggregates proportions, improved aggregate stability, and exhibited higher delta C-13 and delta N-15 values in both bulk soils and aggregate fractions compared to monoculture plantations. In afforested soils, delta C-13 and delta N-15 values increased with increasing aggregate size, while soil C flow pathways progressively shifted from <0.053 mm to 4-8 mm aggregates, leading to higher SOC and STN concentrations within >2 mm aggregates. The enhanced SOC and STN storages under mixed-species afforestation were primarily driven by the increased >2 mm aggregate proportions and their higher associated SOC and STN concentrations, with the former playing a greater role. These processes were strongly associated with improved litter and root quality, and higher soil calcium and magnesium oxides concentrations. However, even after 10 years of mixed-species afforestation, the proportion of >2 mm aggregates, aggregate stability, and SOC and STN storages remained significantly lower than those in the secondary forest. Our results demonstrate that mixed-species afforestation is more effective than monoculture plantations in enhancing soil structural stability and promoting SOC and STN sequestration, supporting its priority in vegetation restoration of degraded karst ecosystems.