AbstractThe 4‐year application of pig‐manure compost (PMC) to crop fields in Jiangsu significantly increased organic‐C and total N concentrations compared to chemical fertilization and control treatment. To identify the soil processes that led to these changes, 13C cross‐polarization magic‐angle spinning nuclear‐magnetic resonance (13C CPMAS NMR) and dipolar‐dephasing nuclear‐magnetic‐resonance spectroscopy (DD NMR) were conducted on soil organic matter (SOM) fractions separated by wet‐sieving and density fractionation procedures. This allowed characterization of the SOM quality under three contrasting fertilizer regimes. The results indicate that PMC application can alter the distribution of functional groups and improve alkyl C‐to‐O‐alkyl C ratios compared to chemical‐fertilizer treatment (CF). Alkyl C contents were increased from macroaggregate fractions (> 2 mm) to microaggregate fractions (0.05–0.25 mm) for all treatments, suggesting that recalcitrant material accumulates in the microaggregate fractions. The O‐alkyl C contents were decreased from macroaggregate fractions (> 2 mm) to microaggregate fractions (0.05–0.25 mm) under CF and PMC treatments, while no consistent trend was found for the control (NF) treatment. The alkyl C‐to‐O‐alkyl C ratios in macroaggregates were lower than those in microaggregates, indicating that the degrees of SOM decomposition were lower in macroaggregates compared to microaggregates. In all aggregate‐size classes, the amount of organic matter appeared to depend on the fertilization regime. This study provides useful information regarding the buildup of organic material in soil from long‐term manure‐compost enrichment.