The humic fractions were sequentially extracted from soils to study the heterogenous properties of soil organic matter (SOM). However, the bulk characteristics of these samples, such as elemental compositions and functional groups, could not fully reveal their diverse compositions. We sequentially extracted humic acids (HAs) from a sediment, and analyzed its molecular markers (benzene polycarboxylic acids (BPCAs), lignin-derived phenols, free lipids and bound lipids) to illustrate the diverse compositions of SOM. Our results suggested that the investigated HAs were derived from terrestrial C3 plants as reflected by the range of their δ13C values (−27.08 ‰ in HA1 to −27.85 ‰ in HA6), more specifically, non-woody tissue of angiosperm and belowground part as suggested by lignin and lipid markers. With the increasing times of extraction, the relative abundances of lignin-derived phenols, free lipids, and bound lipids increased, while those of the condensed aromatics (as indicated by BPCAs) decreased. We also observed that with the increasing times of extraction, the carbon preference index (CPI) increased, the ratios of acids to aldehydes of vanilly units (Ad/Al)v and δ13C of HAs decreased, suggesting that the extensively degraded organic compositions were selectively extracted because of their favored dissolution. Our results emphasize that the complete extraction of organic compositions is essential to ensure reliable analysis on SOM properties and turnover. The distribution of individual BPCAs suggested that the highly condensed aromatics were preferentially extracted. These might be attributed to the less condensed aromatics were more strongly associated with mineral particles, which is important for the protection of aromatic carbons in the environment.