Abstract: Soil organic carbon and aggregates play an important role in soil fertility, crop yield, and the farmland environment, all of which are key components for sustainable agriculture. A wild long-term organic material and mineral fertilizer field experiment was initiated in 2003 at the Luancheng Agroecosystem Experimental Station of the Chinese Academy of Sciences. The experiment sought to investigate how different fertilization patterns affect the soil aggregate composition and the levels of organic carbon in the aggregates to better understand how different agricultural management practices serve as physical protection mechanisms. There were six treatments: no fertilization (i.e., conventional, CK), straw application alone (S), organic manure application alone (M), mineral fertilizer application (NPK), NPK plus straw (SNPK), and NPK plus organic manure (MNPK). The contents of total organic carbon (TOC), soluble organic carbon (DOC), acidolytic active organic carbon (AC), resistant organic carbon (ROC), and labile organic carbon (LOC) were examined within the aggregate fractions, including the total soil, large aggregates (>2 mm), small aggregates (0.25-2 mm), and microaggregates (< 0.25 mm). The results showed that fertilization had a significant effect on the distribution and stability of soil aggregates. SNPK significantly increased the amount of >0.25 mm aggregates. The contents of DOC and ROC were positively correlated with the amount of large aggregates and promoted the formation of large aggregates. Compared with NPK, SNPK and MNPK significantly increased the contents of SOC components in the aggregate fractions, and SNPK addition improved the SOC content compared to MNPK. In the aggregate fractions, the content of each organic carbon component was in the order of small aggregates > large aggregates > microaggregates, and more than 70% of the organic carbon came from the >0.25 mm aggregates. The LOC/TOC ratio in the MNPK and SNPK treatments increased to 14.95% and 15.70%, respectively, which was 11.94% under CK treatment. MNPK was conducive to LOC storage in large aggregates, which improved the soil fertilizer supply capacity; while SNPK promoted LOC migration to the small-sized aggregates, enhanced its stability in the aggregates, and improved the soil fertilizer retention capacity. In conclusion, long-term organic and inorganic fertilizer combined application improved soil carbon storage and stability. The study provides a theoretical basis for a nutrient management strategy with partial substitution of chemical fertilizer by organic manure and straw.