Aluminum toxicity, a major abiotic stress that inhibits plant growth and development, has become one of the main factors reducing agricultural yield. To reveal the physiological mechanism of boron on alleviating aluminum toxicity of Trichosanthes kirilowii Maxim., seedlings from Anguo (with strong Al-tolerance) and Pujiang (with weak Al-tolerance) varieties of T. kirilowii were selected for water culture experiments and the effects of boron treatment (50 μmol/L) on varieties' growth, aluminum accumulation, antioxidant capacity, and cell wall components under aluminum stress (300 μmol/L) were studied. The results showed that 300 μmol/L Al³⁺ stress inhibited the root length, plant height, fresh weight, and dry weight of the plant. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were significantly decreased, and the content of malondialdehyde (MDA) in root tip of T. kirilowii in Anguo and Pujiang varieties increased by 256.1% and 278.2%, respectively. Aluminum stress also significantly enhanced the content of cell wall polysaccharide, pectin methylesterase (PME) activity, and root tip aluminum accumulation. However, the degree of pectin methyl-esterification (DM) and the content of 3-deoxy-d-mannose-octanoic acid (KDO) were strongly inhibited. Exogenous boron could alleviate the inhibitory effect of aluminum stress on the growth of T. kirilowii seedlings. The antioxidant enzyme activities of T. kirilowii in Anguo and Pujiang varieties were increased significantly. The MDA content, cell wall polysaccharide content, and PME enzyme activity were decreased. In addition, the pectin DM value of Trichosanthes in Anguo variety returned to 91.5% of the normal level, and the KDO content of T. kirilowii in Pujiang variety increased by 52.0% compared with that in the single aluminum treatment group. As a result, the active aluminum binding sites decreased, effectively reducing the aluminum content in the root tip and maintaining its morphological structure. Therefore, boron improved the tolerance of T. kirilowii seedlings to aluminum toxic environment by regulating the polysaccharide components of cell wall and stabilizing its grid structure to reduce the absorption of aluminum by root tips, and enhancing the activity of antioxidant enzymes to alleviate the secondary oxidative stress in the growth of T. kirilowii seedlings, which has a better effect on Anguo variety with stronger tolerance to aluminum toxicity. The research in this paper can provide theoretical guidance for improving the environment for crop growth under acid-aluminum stress.