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A combination of solid-state CPMAS-13C-NMR and TMAH thermochemolysis-GC/MS was applied to investigate the molecular composition of particulate organic matter (POM) separated from a Chinese paddy soil, from the Tai Lake region, under a long-term field experiment with different fertilizer treatments. The treatments were: (i) no fertilizer application (NF), (ii) chemical fertilizers only (CF), (iii) chemical fertilizer plus pig manure (CFM) and (iv) chemical fertilizer plus crop straw (CFS). CPMAS-13C-NMR spectra showed that POM from all treated plots was rich in O-alkyl-C compounds, followed by alkyl-C and aromatic-C compounds. However, as compared with a control (NF), POM under CFM and CFS treatments exhibited a smaller relative O-alkyl-C content and a larger contribution of aromatic-C and alkyl-C, thus increasing both aromaticity and hydrophobicity and, hence, recalcitrance of POM samples. Thermochemolysis of POM from all treatments demonstrated a dominance of aliphatic and lignin-derived compounds. However, the distribution of lignin monomers (p-hydroxyphenyl, P, guaiacyl, G, and syringyl, S) revealed significant differences among the treatments. The relative distribution of lignin P, G and S monomers in NF, CF and CFS indicated a preferential contribution of annual crops and maize straw, as compared with that found for CFM. Concomitantly, a larger content of aliphatic thermochemolysis derivatives was found for CFS and CFM. The relative increase of aliphatic molecules in CFS was attributed to hydrophobic polyesters from higher plants. In the CF and CFM systems, the presence of aliphatic components of microbial origin suggested a greater microbial activity in comparison with NF and CFS. The combined application of solid state CPMAS-13C-NMR and TMAH thermochemolysis-GC/MS can be used to assess effectively the accumulation of recalcitrant organic compounds in soil POM under long-term fertilizer application with organic biomass. It is thus inferred that soil organic matter stabilization by molecular recalcitrance contributes to carbon sequestration in Chinese paddy soils under long-term managements.