This study investigated the effect of chemical heterogeneity of humic acids (HAs) on the equilibrium sorption of phenanthrene by HA extracts. Six HA samples were extracted from three different soils with 0.5 M NaOH and 0.1 M Na4P2O7 and were characterized with elemental analysis, infrared spectrometry, and solid-state 13C nuclear magnetic resonance (NMR) spectrometry. The equilibrium sorption measurements were carried out with a batch technique and using the six HA solids as the sorbents and phenanthrene as the sorbate. The measured sorption isotherm data were fitted to the Freundlich equation. The results showed that, for the same soil, (i) the total HA mass extracted with Na4P2O7 was 13.7-22.6% less than that extracted with NaOH, (ii) the Na4P2O7-extracted HA had higher O/C atomic ratio, greater content of polar organic carbons (POC), and lower aliphatic carbon content than the NaOH-extracted HA, and (iii) the Na4P2O7-extracted HA exhibited greater sorption isotherm linearity and but not dramatic difference in sorption capacities than the NaOH extracted HA. The differences in the HA properties resulting from the two different extraction methods may be because NaOH can hydrolyze insoluble HA fractions such as fatty acid like macromolecules bound on soils whereas Na4P2O7 could not. As a result, the HAs extracted with the two different methods had different polarity and functionality which affected their sorption property for phenanthrene.