There is limited information on carbon sequestration efficiency (CSE) of soil aggregates in upland and paddy soils under long-term fertilization regimes.  In a red soil region of southern China, an upland soil experiment started in 1986 and a paddy soil experiment commenced in 1981.  These experiments were conducted using different fertilization treatments.  After 30 years, soil organic carbon (SOC) content and stock of different aggregate components were analyzed.  The results showed that the SOC contents and stocks in upland soil were lower than in paddy soil.  In both upland and paddy soils, the SOC contents and stocks of all aggregate components in NPKM (combined treatment with chemical nitrogen (N), phosphorus (P), potassium (K) fertilizers and manure) were the highest among all treatments.  Compared with CK (no fertilizer), SOC content of all aggregate components in NPKM was increased by 13.21–63.11% and 19.13–73.33% in upland and paddy soils, respectively.  Meanwhile, the change rates in SOC stock of all aggregate components in upland soil were lower than in paddy soil, although the change rate of SOC stock of all aggregate components in NPKM was higher than in other treatments.  Furthermore, a linear equation could fit the relationships between carbon (C) input and change rate of SOC stock (P<0.05).  Results indicated that the sum of CSE from all aggregate components in upland soil (16.02%) was higher than that of paddy soil (15.12%) in the same climatic condition and from the same parent material.  However, the CSEs from all aggregates were higher than that of bulk soil, although the result from bulk soil also showed that the CSE of upland soil was higher than that of paddy soil.