Cocontamination by heavy metals and persistent organic pollutants (POPs) is ubiquitous in the environment. Fate of POPs within soil/water-plant system is a significant concern and an area where much uncertainty still exists when plants suffered cotoxicity from POPs and metals. This study investigated the fate of polybrominated diphenyl ethers (PBDEs) when copper (Cu) was present within the soil/water-plant system using pot and hydroponic experiments. The presence of Cu was found to induce damage to the root cell membranes of corn (Zea mays L. cv. Nongda 108) with increasing concentration in both shoots and roots. The PBDE congeners BDE209 and BDE47 in shoots were also enhanced with the increasing electrolytic leakage from root, attributed to Cu damage, and the highest shoot BDE209 and BDE47 levels were observed under the highest Cu dosage. In addition, positive correlations were observed between the PBDE content of corn shoots and the electrolytic leakage of corn roots. These results indicated that within a defective root system, more PBDEs will penetrate the roots and are acropetally translocated in the shoots. The potential ecological risk associated with the translocation and accumulation of POPs into plant shoots needs careful reconsideration in media cocontaminated with metals and POPs, whereas often ignored or underestimated in environmental risk assessments.