Arbuscular mycorrhizal (AM) fungi play key roles in ecological restoration and ecological reconstruction of degraded ecosystems in arid and semi-arid lands. Based on the previous results of limiting soil moisture and soil available phosphorus (AP) deficit in the arid valley of Mingjiang River, which is one of the main branches of Yangtze River and located in the north of the Hengduan Mountain Systems, a full factorial and completely random pot experiment in a greenhouse was designed and conducted to understand the influence of two AM fungi (Glomus mosseae and Glomus coronatum) on dynamics of Bauhinia faberi seedling growth. We calculated biomass production and its partitioning, inoculation rate, and mycorrhizal growth response (MGR) across one growth season with two soil AP concentration (P1:6.0 and P2: 24.0 mg P/kg soil). The following results were obtained: (1) Irrespective of both low and high soil AP concentration (6.0 mg/kg and 24.0 mg P/kg soil), both AM fungi could well colonized root of B. faberi seedlings. Under two soil AP conditions, growth promotion effects on seedling root, leaf number and biomass production were significantly increased marked when inoculating B. faberi seedling roots with both AM fungi (G. mosseae or G. coronatum); (2) inoculation with G. mosseae or G. coronatum on seedling root significantly impacted on root biomass accumulation and its partitioning (P < 0.05). However, soil AP did a little effect on biomass accumulation and its partitioning (P > 0.05), the coupling interaction between inoculated with AM fungi and soil AP was obvious (P < 0.05) by multivariate analysis of variance (MANOVA); (3) The inoculation rate of G. mosseae ranged from 51% to 71% under low soil AP condition and ranged from 60% to 74% under high soil AP condition, the inoculation rate of G. coronatum did from 30% to 31% under low soil AP condition and from 35% to 58% under high soil AP condition. Therefore, seedling inoculated with G. mosseae had absolutely higher the root length, leaf number, total biomass, inoculation rate, and MGR than those of seedlings inoculated with G. coronatum. The result suggested that G. mosseae is the more appropriate host for B. faberi in poor arid environment; (4) MGR of G. mosseae and G. coronatum was marked increasing, Inoculation with AM fungi can decrease the limiting strengthen of soil AP. Moreover, the extent with age of seedlings (both 48 and 86 day) was apparently more stronger than those seedlings of 104 day. However, no significant higher of inoculation rates for both AM fungi under 6.0 and 24.0 mg P/kg soil condition demonstrated that the impacts of soil AP on inoculation rate of AM fungi was weakly. The different abilities of both AM fungi (G. mosseae or G. coronatum) could improve growth on B. faberi seedling, which indicated that it is important and necessary to select beneficial AM fungi for vegetation restoration practice in multi-resource limiting regions.