Although maintaining/improving soil organic matter (SOM) quantity through utilizing organic amendments (OAs) is a productive practice, information on OA components contributing to long-term SOM accumulation in agricultural soils remains meager. Hence, we examined soil samples from a long-term experiment with different fertilizer managements, including no fertilizer (NF), chemical fertilizer (CF) only (CF), bark compost plus CF (BC + CF), coffee residue compost plus CF (CRC + CF), cattle manure compost plus CF (CMC + CF), and cattle manure compost (CMC) or sewage sludge compost (SSC) alone at a higher application rate. SOM in those samples was physically fractionated into free particulate form (fSOM), free form occluded in aggregates (oSOM), weakly bound form (wSOM), and strongly bound form (sSOM). Analysis of structural components in OAs and SOM fractions using thermally assisted hydrolysis and methylation combined with gas chromatography/mass spectrometry (THM-GC/MS) revealed OA components that have contributed to long-term SOM accumulation in each treatment. The SSC was characterized by higher proportions of short-chain fatty acids (FAs; 50%) and other aliphatic compounds (22%). Correlation analysis suggested that these characteristics may be effective for greater C accumulation in the bulk soil and wSOM fraction. The proportion of lignin-derived phenols, e.g., 3,4-dimethoxybenzaldehyde (Vh) and 1,2-dimethoxy-4-(1,2,3-trimethoxypropyl)benzene, was high in CMC (43%), presumably vital for promoting C accumulations in the oSOM, wSOM, and sSOM fractions in the CMC treatment. The short-chain FAs in CRC and aromatic components in BC are likely important for contributing fSOM accumulation.