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Abstract: We examined the long-term effects of inorganic fertilizer (N and NPK) and manure application on soil aggregation and carbon (C) fractions under a double corn (Zea mays L.) cropping system in a subtropical red soil. Results showed that application of manure combined with NPK (NPK+M) gained the highest yield and increased the stability of crop production. Application of inorganic fertilizer could sustain soil organic carbon (SOC) concentrations, whereas long-term application of manure alone or combined with NPK (M and NPK+M) significantly increased SOC contents compared with the unfertilized control. Manure application significantly increased the proportion of large macroaggregates (>2000µm) compared with the control, while leading to a corresponding decline in the percentage of microaggregates (53–250µm). Carbon storage in the intra-aggregate particulate organic matter within microaggregates (iPOM_m) was enhanced from 9.8% of the total SOC stock in the control to 19.7% and 18.6% in the M and NPK+M treatments, respectively. The shift in SOC stocks towards microaggregates is beneficial for long-term soil C sequestration. Moreover, the differences in the microaggregate protected C (i.e., iPOM_m) accounted, on average, for 39.8% of the differences in total SOC stocks between the control and the manure-applied treatments. Thus, we suggest that the microaggregate protected C is promising for assessing the impact of long-term fertilization management on SOC storage in the red soil. [Copyright &y& Elsevier]