As an important group of persistent organic pollutants (POPs), polychlorinated biphenyls (PCBs) are ubiquitously detected in the environment and greatly threaten the eco-systematic security and human health. To evaluate the risks of PCBs in typical soil matrices, it is of significance to characterize the bioavailability and the relevant molecular mechanism of PCBs. In this paper, Eisenia fetida was used to simulate the accumulation kinetics of six representative PCB congeners, i.e. PCB-18, PCB-20, PCB-28, PCB-101, PCB-105 and PCB-114 in soil, and the effects of earthworm accumulation on the total amount of PCBs in soil was also analyzed. The results showed that 15 d was enough for PCB-18, PCB-20 and PCB-28 congeners to access the near-equilibrium state of whole accumulation kinetics process, while the demanded time was about 30 d for PCB-101, PCB-105 and PCB-114 congeners. The extension of equilibrium time of PCBs with higher chlorination may be attributed to the larger molecular volume of them, so that the free transfer throuth membrane and lipid accumulation was limited, and accordingly the velocity of uptakes decreased. The high linear correlation between the bioavailability and typical molecular properties (α, Kow) of PCBs implicated the influential molecular mechanism on bioavailability from the microcosmic aspects. The molecular volume, polarizability and corresponding hydrophobic interaction were further indicated to be the main effective factors. The study would provide scientific guidelines for the ecological risk prediction and assessment of PCBs in soil.