Boron (B) is indispensable for plant growth and has been reported in the mitigation of aluminum (Al) toxicity in different plants. This study unraveled the efficacy of B in reducing the toxicity of Al to trifoliate orange seedlings in a hydroponic experiment. In the current study, B supply had a positive effect on root length and plant growth-related parameters, and attenuated Al-induced inhibition of plasma membrane H+-ATPase activity. The results of XPS and SEM-EDS revealed that B reduces the Al accumulation in root cell wall (CW), especially acts on pectin fractions (alkali-soluble pectin), accompanied by suppressing the pectin synthesis, inhibiting pectin methylesterase (PME) activity and PME expression. Furthermore, B application inhibits NRAT1 expression while increases ALS1 expression, which are responsible for restraining Al transport from external cells to the cytoplasm and accelerating Al divert to vacuoles, and the results can be further demonstrated by TEM-EDS analysis. Taken together, our results indicated that B mainly promotes the efflux of H+ by regulating the plasma membrane H+-ATPase activity, futhur reduce the demethylation of pectin to weaken Al binding ability to carboxyl. More importantly, B alleviated some of the toxic effects of Al by decreasing the deposition of Al in cytoplasm and compartmentalizes Al into vacuoles.One-sentence summaryBoron can reduce the binding amount of carboxyl group to Al in pectin, decreasing the deposition of Al in cytoplasm and compartmentalizes Al into vacuoles, thereby reduce the toxicity of Al to plants..