Tetramethylammonium hydroxide (TMAH) thermochemolysis-gas chromatography/mass spectrometry (GC/MS) was employed to investigate the supramolecular structure of particulate organic carbon (POC) sampled from a Tai Lake paddy soil under a long-term field experiment with different fertilization systems. The chromatograms revealed peaks related to compounds derived from lignin and aliphatic compounds. The dominant lignin-derived compounds were mainly derivatives of guaiacyl (G) and p-hydroxyphenyl (P) structures, suggesting the contribution of a non-woody (grass) lignin type (mainly crop residues from rice and rape). The most abundant aliphatic compounds were C8-C30 fatty acid methyl esters (FAMEs) dominated by even-numbered carbon species, in which short chain FAMEs of microbial origin were prevalent. Soil fertilizations induced differences of the distribution of each thermochemolysis compound both in bulk soil and water-stable aggregations, and thereby the relative contribution of each compound to the stability of POC. Generally, the lignin compounds and aliphatic compounds of microbial origin contributed to the accumulation and stabilization of POC under the treatment of chemical fertilizer plus pig manure. Nevertheless, the enhanced POC under chemical fertilizer plus crop straw was attributed preferentially to aliphatic compounds of higher plant origin, followed by those of microbe origin. The higher POC content in water-stable aggregates under organic-inorganic fertilization treatments was supposed to be predominantly due to the decomposition of higher plants. The C stabilization by molecular recalcitrance is supposed to contribute to the C sequestration and stabilization in paddy soils under good managements, the relative distribution of which can indicate the different source of newly-accumulated soil organic C.