Improving soil organic C (SOC) has long been recognized as a strategy to reduce soil degradation in agricultural systems. Fertilization has the potential to enhance SOC content and improve soil aggregation. We examined the effects of six fertilization treatments [control (CK), manure (M), phosphorus (P), NP (nitrogen and phosphorus), NPK (nitrogen, phosphorus and potassium) and NPKL (nitrogen, phosphorus, potassium and lime)] on SOC storage and their distribution within aggregate-size fractions in a long-term winter wheat experiment established in 1892 in the south central United States. Collected field soils were wet-sieved into four aggregate-size classes (> 2000μm, 250-2000μm, 53-250μm, and <53μm). Results showed that long-term fertilization significantly affected water-stable aggregate distribution, increasing the content of macro-aggregates (250-2000μm) and micro-aggregates (53-250μm), whereas decreasing that of silt (<53μm) compared with the control treatment. Moreover, applying manure increased the content of macro-aggregate (> 2000μm) compared with other fertilizers. Fertilization increased soil C content by 5.1-50.7% in all the aggregate fractions in the surface 0-15 cm soil  while there was no significant impact on the sub-surface (15–30 cm) soil layer. Manure application increased the SOC concentration in the aggregate fractions compared as compared to the mineral fertilization and control treatments. Organic C concentration generally increased with increasing aggregate size. Overall, long term fertilization, especially manure addition, increases soil water-stable aggregates and improves soil C storage.