Macleaya cordata (Willd.) R. Br. are proposed for the application in phytoremediation of heavy metal-contaminated soil. In this paper, the physiological response, subcellular distribution, chemical form, ultrastructure, and manganese (Mn) absorption characteristics of M. cordata under the stress of 0, 3, 6, 9, 12, and 15mmol/L manganese concentration were studied by sand culture experiment. The results showed that M. cordata seedlings show high tolerance to Mn stress with a concentration of less than 6mmol/L, while higher Mn concentration showed a significant toxic effect. A low concentration of Mn (≤ 6mmol/L) can promote the synthesis of chlorophyll and soluble protein; furthermore, superoxide dismutase and peroxidase activities responded positively. The accumulation of Mn in the inactive metabolic part (cell wall and vacuole) of M. cordata leaves might be one of the main Mn detoxification mechanism. According to the ultrastructure of M. cordata, high-concentration Mn2+ (≥ 12mmol/L) stress can cause M. cordata cells to be distorted and deformed, black precipitates appeared in the intercellular space, mitochondria decrease, chloroplasts shrink, hungry particles increased, and starch granules decrease. The uptake ability of different tissues for Mn is leaf > root > stem, and transport coefficient decreases with the increase of Mn concentration. Clearly, M. cordata has a certain tolerance to manganese, which has the ecological application potential in Mn-polluted areas.