The long-range migration ability of persistent organic pollutants was characterized by both K_OA and P_L. It is difficult for a traditional model of 3D-QSAR to capture the relationship between the double activities of pollutants and their structures. To this end, a log-normalized method was employed to treat a given data set (K_OA and P_L values) to obtain a comprehensive activity (Z) that represents the longrange migration ability of polyhalogenated biphenyls. Then, the relationship between the comprehensive activity of polyhalogenated biphenyls and their structures could be constructed; the proposed model was named the three-dimensional quantitative structure-double-activities relationship (3D-QSA²R) model. Two new PCB-52 molecules with a reduced ability for long-range migration were designed after analyses of the contour maps, with Z values increasing significantly by 30.44-41.30%, and the environmental persistence, bioconcentration and biotoxicity decreased by 3.37-8.99%, 26.86-26.73% and -1.17-3.50%, respectively, compared with those of PCB-52. logK_OA and logP_L values of the novel modified PCB-52 were predicted as 3.20-4.57% and 74.57-79.19%, respectively, by the EPI database software, and these values showed a consistent increasing trend with the Z values predicted by 3D-QSA²R, indicating that the established 3D-QSA²R could be used to deal with the relationship between the multi-activities of organic pollutants and their structures.