Manganese (Mn) is one of the essential microelements in all organisms. However, high level of Mn is deleterious to plants. In this study, the effects of exogenous manganese application on mineral element, polyamine (PA) and antioxidant accumulation, as well as polyamine metabolic and antioxidant enzyme activities, were investigated in Malus robusta Rehd., a widely grown apple rootstock. High level of Mn treatments decreased endogenous Mg, Na, K and Ca contents, but increased Zn content, in a Mn-concentration-dependent manner. Polyamine metabolic assays revealed that, except the content of perchloric acid insoluble bound (PIS-bound) spermine, which increased significantly, the contents of putrescine (Put), spermidine (Spd) and spermine (Spm) all decreased progressively, accompanied with the decreased activities of arginine decarboxylase (ADC, EC 4.1.1.19) and ornithine decarboxylase (ODC, EC 4.1.1.17), and the increased activities of diamine oxidase (DAO, EC 1.4.3.6) and polyamine oxidase (PAO, EC 1.5.3.3). Further antioxidant capacity analyses demonstrated that contents of anthocyanin, non-protein thiols (NPT) and soluble sugar, and the activities of guaiacol peroxidase (POD, EC 1.11.1.7), catalase (CAT, EC 1.11.1.6) and superoxide dismutase (SOD, EC 1.15.1.1), also increased upon different concentrations of Mn treatments. Our results suggest that endogenous ion homeostasis is affected by high level of Mn application, and polyamine and antioxidant metabolism is involved in the responses of M. robusta Rehd. plants to high level of Mn stress.