Rape (Brassica napus L.) seedling pot experiments were performed with a red soil treated with goethite which had boron (B) either adsorbed (ad-B-goethite) or occluded (oc-B-goethite). Soil acidity, different forms of manganese in the soils and different elements content of the rape seedlings were determined. It was found that the addition of boron-containing goethite to the soils resulted in increased rape growth, elevated soil pH and decreased exchangeable acidity. Compared with the control, boron-containing goethite elevated the content of exchangeable manganese (Mn) (EXC-Mn), organic matter bound Mn (OM-Mn), reducible oxide Mn (RO-Mn) and residual Mn (RES-Mn) which were difficult to use for plant. Low labile organic matter was significantly correlated with easily reducible oxide Mn (ERO-Mn) (P < 0.01) and RO-Mn (P < 0.05). Middle organic matter and soil pH was significantly (P < 0.05) correlated with RES-Mn. Stepwise regression was used to select the combination of variables that best estimates shoot and root dry weight of rape seedling. Among them, soil pH, EXC-Mn, OM-Mn, RO-Mn and RES-Mn significantly influenced the dry weight of rape seedlings. The addition of boron-containing goethite improved the uptake of iron (Fe), calcium (Ca), magnesium (Mg), and copper (Cu) element and decreased the uptake of Mn and zinc (Zn) element in rape seedling. The results suggested that boron-containing goethite could provide a better soil acidity environment for plant growth; it was also an important agent increasing a part of manganese difficult to use for plant and reducing the activity of soil manganese, which was beneficial to altering rape seedling growth.