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Effective phytoremediation of Mn contaminated soil requires the selection of a species with good manganese tolerance. Broussonetia papyrifera is an important economic plant and pioneer species, it could be well adapted to drought and saline-alkali environment. In order to understand the effect of Mn stress on B. papyrifera, the effects of different concentrations of Mn (0–50 mmol/L) stress on the growth, morphology, Mn tolerance and physiological indexes of the plant were explored. The results showed that the biomass, surface area, length, root volume, tips, forks, and crossings of B. papyrifera reached the maximum at the Mn concentration of 1 mmol/L. Mn content in the tissue and TF in plants increased with the increase of concentration, while the BCF increased first and then decreased, and the maximum BCF was 0.154 at 10 mmol/L. The accumulation of Mn lead to cell membrane lipid peroxidation, which increased toxic substances in plants, resulting in the increase of MDA and PRO, and affected the synthesis of chlorophyll. However, B. papyrifera could effectively alleviate oxidative stress by increasing the activities of antioxidant enzymes (SOD, POD, CAT), protein and soluble sugar. The results suggested that B. papyrifera had a good oxidative stress mechanism to Mn stress and could be used as candidates for remediation of pollution in mining areas.