Dissolved organic matters (DOM) have important influence on the environmental behavior and fate of organic pollutants, therefore rationalization of interaction mechanisms between pollutants and DOM has become a hot topic in the field of environmental studies. In this paper, polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs), widely detected pollutants, were chosen as target compounds. The effects of substituent position on the interaction between PBDEs/PCBs and DOM were explored. Equilibrium dialysis technique combined with quantum chemistry and molecular docking calculations were employed to reveal the interaction mechanism from the view of charge distribution and molecular conformation. It is shown that non-ortho-substituted isomers have larger volumes and stronger hydrophobicity than those of ortho-substituted, therefore non-ortho-substituted isomers bind more favorably with DOM by hydrophobic partition. By calculating the atomic charge distribution of target chemicals and Leonardite humic acid (LHA) molecular model, π-πinteractions between the aromatic rings of target chemicals with LHA are proposed and further proved in molecular docking calculations. There were 10, 8, 6 docking conformations demonstrating π-πinteraction with LHA for CB-77, BDE-77 and BDE-47, respectively, but none was found for CB-47. By comparing the change of dihedral angle of the aromatic rings and energy barrier, non-ortho-substituted PBDEs/PCBs have larger dihedral angle adjustment space and flexibility, which results in stronger interaction and binding capability with DOM than ortho-substituted isomers. This paper shed some lights on the effect of substituent position on the environmental behaviors of PBDEs and PCBs.