The effects of the chemical structure, surface properties, and micropore of modified black carbon samples (BCs) on the sorption mechanism of hydrophobic organic contaminants (HOCs) are discussed. Activated and oxidized BCs were produced from a shale kerogen at 250-500 °C by chemical activation regents (KOH and ZnCl2) and then by oxidative regents (H2O2 and NaClO). The surface properties (water contact angel, Boehm titration, and cation exchange capacity, CEC), structural properties (advanced solid-state 13C NMR), micropore properties (CO2 adsorption), mesopore properties (N2 adsorption), and sorption and desorption properties of phenanthrene were obtained. The results showed that ZnCl2-activated BCs had higher basic surface groups, CEC values, aromatic carbon contents, micropore volumes, and adsorption volumes but exhibited lower acidic surface groups than the KOH-activated BCs did. Micropore modeling and sorption irreversibility indicated that the micropore filling was the main sorption mechanism of phenanthrene. In addition, ZnCl2 activated and NaClO oxidized BCs showed a nice regression equation between adsorption volumes and micropore volumes (CO2- V0) as follows: Q0' = 0.495 V0 + 6.28( R2 = 0.98, p < 0.001). Moreover, the contents of nonprotonated aromatic carbon, micropore volumes, and micropore sizes are the critical factors to micropore filling mechanism of phenanthrene on BCs. The size of fused aromatic rings was estimated from the recoupled 1H-13C dipolar dephasing, and the BC structural models at temperatures ranging from 300 to 500 were proposed. This finding improves our understanding of the sorption mechanism of HOCs from the perspectives of chemical structure and micropore properties.