The lack of clarity of how natural vegetation restoration influences soil organic carbon (SOC) content and SOC components in soil aggregate fractions limits the understanding of SOC sequestration and turnover in forest ecosystems. The aim of this study was to explore how natural vegetation restoration affects the SOC content and ratio of SOC components in soil macroaggregates (>250 μm), microaggregates (53–250 μm) and silt and clay (<53 μm) fractions in 30-, 60-, 90- and 120-year-old Liaodong oak (Quercus liaotungensis Koidz.) forests, Shaanxi, China in 2015. And the associated effects of biomasses of leaf litter and different sizes of roots (0–0.5, 0.5–1.0, 1.0–2.0 and >2.0 mm diameter) on SOC components were studied too. Results showed that the contents of high activated carbon (HAC), activated carbon (AC) and inert carbon (IC) in the macroaggregates, microaggregates and silt and clay fractions increased with restoration ages. Moreover, IC content in the microaggregates in topsoil (0–20 cm) rapidly increased; peaking in the 90-year-old restored forest and was 5.74 times higher than AC content. In deep soil (20–80 cm), IC content was 3.58 times that of AC content. Biomasses of 0.5–1.0 mm diameter roots and leaf litter affected the content of aggregate fractions in topsoil, while the biomass of >2.0 mm diameter roots affected the content of aggregate fractions in deep soil. Across the soil profile, macroaggregates had the highest capacity for HAC sequestration. The effects of restoration ages on soil aggregate fractions and SOC content were less in deep soil than in topsoil. In conclusion, natural vegetation restoration of Liaodong oak forests improved the contents of SOC, especially IC within topsoil and deep soil. The influence of IC on aggregate stability was greater than the other SOC components, and the aggregate stability was significantly affected by the biomasses of litter and 0.5–1.0 mm diameter roots in topsoil and >2.0 mm diameter roots in deep soil. Natural vegetation restoration of Liaodong oak forests promoted SOC sequestration by soil macroaggregates.