Polygonum perfoliatum L. is a Mn-tolerant plant as considered having the potential to revegetate in manganese mine wasteland. The glasshouse experiments were carried out to evaluate its tolerance and physiological response in different Mn concentrations (5, 500, 1000, 2000, 5000, and 10,000 μmol L). Absorption bands of P. perfoliatum differed greatly in lipids, proteins, and carbohydrates. With elevated levels of Mn (5-2000 μmol L), absorbance changed little, which demonstrated that lower Mn concentrations had negligible influence on transport functions. As Mn concentrations in excess of 2000 μmol L, absorbance increased slightly but eventually decreased. Furthermore, a hydroponic culture was carried out in order to study its changes of ultrastructure with the increasing Mn concentrations (5, 1000, and 10,000 μmol L). Lower Mn levels with 5 and 1000 μmol L had no breakage function to the ultrastructure of P. perfoliatum. However, as Mn concentration was up to 10,000 μmol L, visible damages began to appear, the quantity of mitochondria in root cells increased, and the granum lamellae of leaf cell chloroplasts presented a disordered state. In comparison with the controls, black agglomerations were found in the cells of P. perfoliatum under the controlling concentration of Mn with 1000 and 10,000 μmol L for 30 days, which became obvious at higher Mn concentrations. As Mn concentration was 10,000 μmol L, a kind of new acicular substance was developed in leaf cells and intercellular spaces, possibly indicating a resistance mechanism in P. perfoliatum. These results confirm that P. perfoliatum shows potential for the revegetation of abandoned manganese tailings.