In tropical Asia, multiple annual cropping of lowland rice and the associated submerged soil conditions have been linked to long-term changes in nitrogen (N) cycling and the chemical nature of soil organic matter. To identify changes in organic matter properties, two humic acid fractions and whole soil samples were obtained from field treatments of lowland rice that varied in cropping intensity, fertilizer management, and location. These samples were methylated and analyzed by pyrolysis-gas chromatography-mass spectrometry. With compounds expressed in relative abundance, whole soil was enriched in nonmethoxybenzene compounds and heterocyclic N compounds compared with extracted humic acids. The young mobile humic acid (MHA) fraction had a wide diversity of methoxybenzenes that are associated with lignin residues. The more recalcitrant calcium humate (CaHA) fraction had characteristics intermediate between whole soil and MHA. Under intensified cropping and increased soil submergence, lignin residues increased in relative abundance in all three fractions. Heterocyclic N compounds decreased with intensified cropping, consistent with previous analysis by 15N nuclear magnetic resonance spectroscopy. Their parent compounds may be primarily naturally occurring heterocyclic N compounds. For whole soil, and especially the MHA, submergence effects were accentuated in treatments with high fertilizer rates, trends that may be related to the balance between input rates and degradation rates of crop residues. The ratio of myristic acid: stearic acid varied with soil submergence, fertilizer rate, and type of fraction in patterns following the abundance of methoxybenzenes. In general, responses of the MHA and CaHA to field treatments were representative of whole soil.