Iron-based nanomaterials hold promise for in situ remediation of persistent halogenated contaminants such as dioxin-like polychlorinated biphenyls, however, their complex interactions and joint toxicity toward beneficial soil biological functions remain unknown. This study examined the effects of nano-zero valent iron (nZVI) on the physiological and morphological changes, on the bioaccumulation of co-existed dioxin-like 3,3′,4,4′-tetrachloro-biphenyls (PCB77), and the joint toxicity of nZVI and PCB77 in earthworms Eisenia fetida. An orthogonally designed experiment was conducted through the exposure of E. fetida to the combined and separate nZVI and PCB77 at various concentrations in soil for 28 days (nZVI at the levels of g-Fe/kg-soil and PCB77 at the levels of mg-PCB/kg-soil). Results indicated that both nZVI and PCB77 inhibited the growth and reproduction of earthworms, and the combined exposure resulted in a synergistic effect. The addition of 10 g/kg nZVI decreased the contents of PCB77 and significantly increased the accumulation of PCB77 to a level ranging 14–97 mg/kg in earthworms in a nZVI dose dependent manner. The observed synergism might relate to the aggravated damage of earthworm epidermis in the presence of nZVI. PCB77 and nZVI at their corresponding high levels (10 mg/kg and 10 g/kg) induced oxidative stress and lipid peroxidation in the earthworms through the increased levels of reactive oxygen species and the subsequent inhibition of antioxidant enzymes including superoxide dismutase and catalase. Further metabolomics analyses revealed that the normal glutamic acid metabolism and tricarboxylic acid cycle were disturbed in earthworms exposed to the combined treatment of 10 mg/kg PCB77 and 10 g/kg nZVI. Our findings suggested that earthworms as a sentinel species could be readily employed in toxicity and tolerance studies to succeed the safe applications of nZVI and interestingly earthworms themselves also hold promise for vermiremediation owing to the high bioaccumulation potential of PCBs from contaminated soils.