Aluminum (Al) toxicity is the main constraint of root growth and productivity on arable acidic soil. Although boron (B) is used to ameliorate Al stress, the exact mechanisms underlying the effects of B on Al-induced alteration on root metabolites are poorly understood, especially in the trifoliate orange, which is an important rootstock in China. Therefore, a hydroponics experiment was conducted to explore the mechanisms of B mitigates Al toxicity in roots of citrus by metabolomics. A total of 60 metabolites were identified and analyzed in the present study. The 17 amino acids and 8 sugars were up-regulated in Al-treated roots, mainly histidine, cycloleucine, asparagine, citrulline, raffinose and trehalose, and increased by 38.5-, 8.7-, 6.0-, 6.0-, 7.5- and 6.6-fold, respectively. Meanwhile, significant down-regulation of aspartic acid, isoleucine, glutamic acid and six sugars were indicated under Al stress. Aluminum induced a decrease of nine organic acids, especially l-malic acid, citric acid and threonic acid, by 98.2, 93.6 and 95.1%, respectively. Interestingly, in the presence of Al, B application decreased the contents of asparagine, cycloleucine, citrulline and histidine as well as myo-inositol, raffinose, galactinol and 3,6-anhydro-d-galactose by 52.2, 57.4, 46.7, 63.0, 65.4, 74.3, 62.5 and 55.0%, respectively. However, there was no obvious difference in the organic acid contents in Al-stressed roots treated with B. Conclusively, our results show that B regulates the metabolic patterns of amino acids and carbohydrates and reduces Al toxicity. Nevertheless, B addition did not affect the Al-induced changes in the metabolic modes of organic acids.