Multi-walled carbon nanotubes (MWCNTs) and heavy metals could be absorbed and bioaccumulated by agricultural crops, implicating ecological risks. Herein, the present study investigated the ecotoxicological effects and mechanisms of individual carboxylated MWCNTs (MWCNTs-COOH) (2.5, 5.0 and 10 mg/L) and their combination with 20 µM Pb and 5 µM Cd (shortened as Pb + Cd) on roots of Vicia faba L. seedlings after 20 days of exposure. The results showed that the tested MWCNTs-COOH induced imbalance of nutrient elements, enhanced isozymes and activities of superoxide dismutase (SOD), guaiacol peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), resulting in accumulation of carbonylated proteins, elevation of endoproteases (EPs) isozymes, and reduction of HSP70 synthesis in the roots. However, the tested MWCNTs-COOH facilitated the enrichment of Cd, Pb and Na elements, contributing to the decrease of SOD, CAT and APX activities, and the reduction of HSP70 synthesis, whereas the elevation of carbonylated proteins, EP activities and cell necrosis in the roots when Pb + Cd was combined in comparison to the treatments of MWCNTs-COOH, or Pb + Cd alone. Thus, the tested MWCNTs-COOH not only caused oxidative stress, but also aggravated the oxidative damage in the roots exposed to Pb + Cd in the culture solution.