Metal-induced oxidative stress in contaminated soils affects plant growth. In the present study, we evaluated the role of seed endophyte FXZ2 on Zn/Cd tolerance and accumulation. A series of pot experiments were conducted under variable Zn (500, 1,000, and 1,500 mg kg) and Cd (5, 15, 30, and 60 mg kg). The results demonstrated that FXZ2-inoculation significantly enhanced the growth of and improved its chlorophyll and GSH content. In the rhizosphere, FXZ2 inoculation changed the chemical speciation of Zn/Cd and thus affected their uptake and accumulation in host plants. The exchangeable and carbonate-bound fractions (F1 + F2) of Zn decreased in the rhizosphere of FXZ2-inoculated plants (E+) as compared to non-inoculated plants (E-) under Zn stress (500 and 1,000 mg kg), correspondingly, Zn in the shoots of E+ decreased ( < 0.05). However, at Cd stress (30 and 60 mg kg), the F1 + F2 fractions of Cd in E+ rhizospheric soils increased; subsequently, Cd in the shoots of E+ increased ( < 0.05). FXZ2 could exogenously secrete phytohormones IAA, GA, and JA. The study suggests that seed endophyte FXZ2 can increase Zn/Cd tolerance of host plant by altering Zn/Cd speciation in rhizospheric soils, as well as exogenous production of phytohormones to promote growth, lowering oxidative damage while enhancing antioxidant properties. For Zn/Cd accumulation, it has opposite effects: Zn uptake in E+ plants was significantly ( < 0.05) decreased, while Cd accumulation in E+ plants was significantly ( < 0.05) increased. Thus, FXZ2 has excellent application prospects in Cd phytoextraction and decreasing Zn toxicity in agriculturally important crops.