We investigated the effects of 16 years long-term fertilizer experiment on aggregate size distribution and the carbon in aggregates of a Drab Fluvo-aquic soil in Beijing. Six treatments were chosen for this work: Four were in a wheat-maize rotation receiving either no fertilizer (CK), mineral fertilizers (NPK), mineral fertilizers plus farmyard manure (NPKM) or mineral fertilizers with maize straw incorporated (NPKS). One was in a wheat-maize/wheat-soybean rotation receiving NPK (NPKF). The other was abandoned arable land (CK0) growing weeds. The amount of chemical fertilizer applied per year was 150 kg N hm-2, 75 kg P2O5 hm-2, 45 kg K2O hm-2, 22.5 t manure hm-2 and 2.25 t maize straw hm-2. Soil samples were separated into four aggregate-size classes (>2mm, 0.25-2mm, 0.053-0.25mm and <0053mm). The results shows than the amount of >2mm water-stable aggregates and organic carbon were found to be higher in long-term abandoned arable land than those in cultivated arable land soils. Macro-aggregates are more susceptible to disruptive forces induced by cultivation, which are less than micro-aggregates. Compared to no fertilizer application treatment (CK), long-term fertilizer application (NPK, NPKM and NPKS) had a significant influence on aggregate size distribution and aggregate stability, and had most effectively accelerate the formation of groups of >2mm and 0.25-2mm aggregates, that show the newly enriched organic carbon mostly appeared in aggregate fractions >2mm and 0.25-2mm.The SOC concentration was greater for macro-aggregates (>2mm and 0.25-2mm) than micro-aggregates (0.053-025mm and <0.053mm) in the abandoned arable land and cultivated arable land soils. After applying mineral fertilizers plus farmyard manure (NPKM), the contents of macro-aggregates increased significantly, being beneficial to the improvement of soil structure. The content of SOC in aggregates was higher in wheat-maize/wheat-soybean rotation cropping system compared to continuous wheat-maize cropping system.