Aluminum (Al) toxicity is a major factor limiting plant productivity. The objective of the present study was to develop the mechanisms of boron (B) alleviating aluminum toxicity in citrus. The results showed that aluminum toxicity severely hampered root elongation. Interestingly, under aluminum exposure, boron supply improved superoxide dismutase activity while reducing peroxidase, catalase and polyphenol oxidase activities. Likewise, the contents of H2O2, lipid peroxidation, protein and proline in roots were markedly decreased by boron application under aluminum exposure. Our results demonstrated that boron could alleviate aluminum toxicity by regulating antioxidant enzyme activities in the roots.