The study examined the influence of compost and mineral fertilizer application on the content and stability of soil organic carbon (SOC). Soil samples collected from a long-term field experiment were separated into macroaggregate, microaggregate, and silt + clay fractions by wet-sieving. The experiment involved seven treatments: compost, half-compost N plus half-fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and control. The 18-year application of compost increased SOC by 70.7-121.7%, and mineral fertilizer increased by 5.4-25.5%, with no significant difference between control soil and initial soil. The C mineralization rate (rate per unit dry mass) in microaggregates was 1.52-2.87 mg C kg(-1) day(-1), significantly lower than in macroaggregate and silt + clay fractions (P < 0.05). Specific C mineralization rate (rate per unit SOC) in silt + clay fraction amounted to 0.48-0.87 mg C g(-1) SOC day(-1) and was higher than in macroaggregates and microaggregates. Our data indicate that SOC in microaggregates is more stable than in macroaggregate and silt + clay fractions. Compost and mineral fertilizer application increased C mineralization rate in all aggregates compared with control. However, compost application significantly decreased specific C mineralization rate in microaggregate and silt + clay fractions by 2.6-28.2% and 21.9-25.0%, respectively (P < 0.05). By contrast, fertilizer NPK application did not affect specific C mineralization rate in microaggregates but significantly increased that in silt + clay fractions. Carbon sequestration in compost-amended soil was therefore due to improving SOC stability in microaggregate and silt + clay fractions. In contrast, fertilizer NPK application enhanced SOC with low stability in macroaggregate and silt + clay fractions.