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Fertilizer sources may have variable effects on soil aggregation, aggregated-associated C and N, and wheat yield. A 34-year field experiment was performed to evaluate the influences of chemical and organic fertilization on soil aggregates and associated carbon and nitrogen under winter wheat in a Cumulic Haplustoll of the Loess Plateau, China. Treatments included unfertilized control (CK), inorganic N fertilizer (NF), inorganic P fertilizer (PF), inorganic N and P fertilizer (NP), organic manure (M), inorganic N fertilizer plus manure (NM), inorganic P fertilizer plus manure (PM), and inorganic N plus P fertilizers plus manure (NPM). Compared to CK, long-term fertilization significantly increased the proportion of soil macro-aggregates, mean weight diameter (MWD), and geometric mean diameter (GMD), but decreased the proportion of micro-aggregates and fractal dimension, especially fertilizer plus manure. Compared to CK, manure treatments (M, NM, PM, and NPM) had a better improvement on soil organic carbon (SOC), soil total nitrogen (STN), particle organic C, and microbial biomass C in all aggregates than the fertilizer alone. The SOC in different aggregates increased with the increased aggregate size, which was because the larger aggregates formed by the binding of the smaller aggregates and organic matter. PON increased in NM and NPM, and MBN was more sensitive to N fertilizer. The C/N ratio in bulk soil and aggregates decreased with fertilization, especially in fertilizer with manure and in macro-aggregates. The improved soil structure was related to the increased SOC and STN, which was proved by the positive correlations among SOC and STN with macro-aggregates and MWD. A correlation analysis also showed that the contribution rate of SOC and STN in macro-aggregates was positively associated with the macro-aggregate and stability. Therefore, the sequestration of C and N in soil was related to aggregate size and was mainly affected by larger aggregates. The results demonstrated that fertilizer with manure improved the soil structure and fertility better than fertilizer alone, thus increasing crop yield. [ABSTRACT FROM AUTHOR]