Copper (Cu) is an essential heavy metal for plants, but high Cu concentration in the soil causes phytotoxicity. Some plants, however, possess a system that can overcome Cu toxicity, such as Cu localization, and an active antioxidant defence system to reduce oxidative damage induced by high Cu concentration. The present study was conducted to explore the phytoremediation potential, morpho-physiological traits, antioxidant capacity, and fibre quality of jute (Corchorus capsularis) grown in a mixture of Cu-contaminated soil and natural soil at ratios of 0:1 (control), 1:0, 1:1, 1:2 and 1:4. Our results showed that high Cu concentration in the soil decreased plant growth, plant biomass, chlorophyll content, gaseous exchange, and fibre yield while increasing reactive oxygen species (ROS), which indicated oxidative stress induced by high Cu concentration in the soil. Antioxidant enzymes, such as superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) scavenge ROS in plant cells/tissues. Furthermore, high Cu concentration did not significantly worsen the fibre quality of C. capsularis, and this plant was able to accumulate a large amount of Cu, with higher Cu accumulation in its shoots than in its roots. Transmission electron microscopy (TEM) revealed that Cu toxicity affected different organelles of C. capsularis, with the chloroplast as the most affected organelle. On the basis of these results, we concluded that high Cu concentration was toxic to C. capsularis, reducing crop yield and plant productivity, but showing little effect on plant fibre yield. Hence, C. capsularis, as a fibrous crop, can accumulate a high concentration of Cu when grown in Cu-contaminated sites.