Based on dry and wet sieving sequences, water-stable aggregates were separated from bulk soils sampled at Chinese FACE (Free-air CO2 enrichment) Platform. The experiment was set as two main treatments: atmospheric CO2 and elevated CO2 and two sub-treatments: low amount of nitrogen fertilizer (LN) and normal amount of nitrogen fertilizer (NN). The effects of elevated CO2 on soil aggregation, soil organic carbon contents (SOC) in aggregates were studied and analyzed. It showed that after 9 years, elevated CO2 increased soil organic carbon by 1% per year. At the 0?–?5 cm soil depth, macroaggregates (>250 μm) tended to break down and thus forming more microaggregates (250 – 53μm ) (27.49%, P = 0.05) under elevated CO2; NN decreased the amount of large macroaggregates (>2 000 μm) of 5 – 15 cm soil by 20.60% (P<0.05). Elevated CO2 had a positive effect on SOC in microaggregates (31.30%, P<0.05), and a negative effect on SOC in small macroaggregates (2 000 – 250 μm) (9.67%, P<0.01) at 0 – 5 cm soil depth; the interaction effect of CO2 and N had a trend to enhance such changes. Elevated CO2 increased SOC of large macroaggregates (26.44%, P = 0.05) and decreased SOC of small macroaggregates (6.83%, P<0.01) at the 5 – 15 cm soil depth; NN decreased SOC in large macroaggregates at 5 – 15 cm soil depth by 30.19% (P<0.001); the interaction effect of CO2 and N decreased SOC in macroaggregates. Elevated CO2 decreased the storage of SOC in small macroaggregates (6.41%, P<0.01) and increased the storage of SOC in microaggregates (15.09%, P<0.05) of surface soil (0 – 15 cm); NN decreased the storage of SOC in macroaggregates; the interaction effect of CO2 and N decreased the storage of SOC in small macroaggregates (P<0.05).