Although leveraging the interaction with endophytic fungi is an efficient and environment-friendly strategy for plants to enhance growth and resistance, how different endophyte species influence host plants’ resilience in adverse conditions remain comparatively unclear. In order to explore the effect of endophytic fungi on the aluminum resistance of woody host plants, Vernicia montana seedlings were subjected to different aluminum concentrations (T0, T1, T2, T3, T4) in this study. The aluminum contents in roots, leaves and rhizospheric soil of V. montana seedlings were determined after applying endophyte suspensions of Pestalotiopsis (NP), Alternaria (LA), Penicillium (QP), Coniothyrium (DC) and Thermophilic (ST) spp. The results showed that aluminum stress treatment, endophytic fungi treatment and their interaction had significant effects on aluminum content in leaves, aluminum content in roots, aluminum content in rhizospheric soil, and the transport and retention rate of aluminum ions in soil-root-leaf. With the increase of aluminum concentrations, the aluminum content in leaves of V. montana increased in the endophyte treatments of LA and ST, decreased in CK, NP and DC, or had marginal variation in QP treatment. Compared with T0, four endophyte treatments of LA, QP, DC and ST significantly reduced root aluminum content under T4 concentration (P < 0.05), contrary to the results of NP treatment. Endophyte treatments significantly increased root aluminum content of V. montana under T1 concentration (P < 0.05). The foliar Al content in fungi-inoculated seedlings was significantly lower than that of the non-inoculated ones under T0 and T3 levels (P < 0.05), the LRR is less than 1, while the opposite trend was observed under T2 and T4 treatments. The aluminum transport coefficient TFsoil-root and TFroot-leaf increased in different proportions under the same aluminum concentration. The findings indicate that the application of endophytic fungi change the aluminum contents and transport from rhizospheric soil, roots to leaves. The specific effects of endophytic fungi vary with the degree of aluminum stress and the fungi genus. The study proves that inoculation of endophytic fungi can improve the aluminum tolerance of host plants, and thereby play an important role in promoting the sustainable development of forestry.