Characterizing pseudo equilibrium-status soil/vegetation partition coefficient KSV, the quotient of respective concentrations in soil and vegetation of a certain substance at remote background areas, is essential in ecological risk assessment, however few previous attempts have been made for field determination and developing validated and reproducible structure-based estimates. In this study, KSV was calculated based on measurements of seventeen 2,3,7,8-substituted PCDD/F congeners in soil and moss (Dicranum angustum), and rouzi grass (Thylacospermum caespitosum) of two background sites, Ny-Ålesund of the Arctic and Zhangmu-Nyalam region of the Tibet Plateau, respectively. By both fugacity model and stepwise regression of field data, the air-water partition coefficient (KAW) and aqueous solubility (SW) were identified as the influential physicochemical properties. Furthermore, validated quantitative structure–property relationships (QSPR) model was developed to extrapolate the KSV prediction to all 210 PCDD/F congeners. Molecular polarizability, molecular size and molecular energy were demonstrated leading effects on KSV.