Bauhinia faberi via. Microphylla (BFM) is an important tree species for vegetation restoration in the dry valley of southwestern China. However, there were few studies on the application of arbuscular mycorrhizal fungi (AMF) in improving the drought adaptation of BFM. In order to investigate the response of BFM to water stress (WS), we tested four inoculation treatments ((no AMF, Control), Glomus mosseae (GM), Glomus intraradices (GI), Glomus mosseae + Glomus intraradices (GMI)) in pots, experimented under three field water holding capacity (WHC) of 70%, 50% and 30%. The changes of seedling survival rate (SR), AMF relative root length colonization rate (Col), growth, photosynthetic parameters, water status and leaf nutrients were examined. The results showed that under 30% WHC drought conditions, SR with dual inoculation of AMF was not higher than with single inoculation of GM, suggesting that increasing the diversity of AMF did not definitely improve plant SR, and that the species of inoculated AMF might have an important impact on SR. The sensitivity of dual inoculated Col to water stress was lower than that of single inoculation, which was more favorable for dual inoculated BFM seedlings adapting to drought environment. The overall drought resistance ability (D) also showed that dual inoculation of AMF improved plant drought adaptation compared with single inoculation, which was related to the higher Col of dual inoculated AMF. This study is of practical importance to promote vegetation restoration in arid areas in a cost-effective and environmentally friendly manner.