To date, there is limited knowledge on the methoxylation of polychlorinated biphenyls (PCBs) and the relationship between hydroxylated polychlorinated biphenyls (OH-PCBs) and methoxylated polychlorinated biphenyls (MeO-PCBs) in organisms. In this study, rice (Oryza sativa L.) was chosen as the model organism to determine the metabolism of PCBs in plants. Limited para-substituted 4'-OH-CB-61 (major metabolite) and 4'-MeO-CB-61 (minor metabolite) were found after a 5-day exposure to CB-61, while ortho- and meta-substituted products were not detected. Interconversion between OH-PCBs and MeO-PCBs in organisms was observed for the first time. The demethylation ratio of 4'-MeO-CB-61 was 18 times higher than the methylation ratio of 4'-OH-CB-61, indicating that formation of OH-PCBs was easier than formation of MeO-PCBs. The transformation products were generated in the roots after 24 h of exposure. The results of in vivo and in vitro exposure studies show that the rice itself played a key role in the whole transformation processes, while endophytes were jointly responsible for hydroxylation of PCBs and demethylation of MeO-PCBs. Metabolic pathways of PCBs, OH-PCBs, and MeO-PCBs in intact rice plants are proposed. The findings are important in understanding the fate of PCBs and the source of OH-PCBs in the environment.