Four humic acids (HAs) including de-ashed HAs (D-HAs), two humins (HMs), nonhydrolyzable carbons, and demineralized fraction (DM) were isolated separately from two soils and characterized detailedly; then their sorption of phenanthrene (Phen) was examined. The sequence of removal of HAs and minerals affected molecular composition of HMs. After de-ashing, thermal stability of HAs was improved; however, sorption (logKoc) also decreased due to removal of amorphous alkyl-C. Significant correlations between CO2 surface area of HAs with their sorption coefficients (n and Koc) suggested that pore filling could dominate Phen sorption. Alkyl-C could facilitate elevated thermal stability of OM and Phen sorption, supporting that thermal stability of OM was correlated with Phen sorption. The OM fraction composed of aromatic moieties (AMs) did not produce the highest logKoc, providing strong evidence to dispute the dominant role of AMs in Phen sorption. No correlations between the Koc values of Phen by all tested sorbents and their bulk or surface polarity were observed, suggesting that the role of bulk or surface polarity of OM fractions in regulating Phen sorption was dependent on soil sources. This work shows the major influence of bulk and surface composition of OM and amorphous alkyl-C isolated from a soil sample on hydrophobic organic compounds sorption.