Among various environmental stresses, drought stress has become a critical problem worldwide due to its dramatic effects on plant growth and physiology, and recently, this has attracted much attention. Arbuscular mycorrhizal fungi (AMF) have previously been reported to afford greater resistance to drought stress in some plant species. The aim of this study was to determine the impacts of AMF on growth and photosynthetic characteristics of Nyssa yunnanensis seedlings through addition (Low AMF) or non-addition (High AMF) of the fungicide benomyl at each water treatment. We further aimed to elucidate drought resistance and associated microbiological mechanisms of this endangered plant species, which would help to establish and implement protection measures. In this study, a pot experiment was conducted to control the soil water content, and 100, 91.68, 82.85, 60.00, 41.86, and 21.28% of field moisture capacity were set. The seedlings were subjected to different watering regimes and measurements were made at the end of the experiment to investigate the growth and photosynthetic characteristics of N. yunnanensis seedlings. Plasticity index analysis and principal component analysis of 18 indices of N. yunnanensis were integrated and analyzed using the membership function method to evaluate synthetic drought resistance. These variables provide a theoretical basis for a better understanding of the mechanism of AMF on the tolerance of N. yunnanensis seedlings to drought stress. The results showed that the AMF colonization rate of N. yunnanensis roots significantly decreased under "Low AMF" treatments, indicating that differences in the growth and photosynthetic characteristics of AMF-treated seedlings were caused by a reduction in the rate of AMF colonization in N. yunnanensis roots. With the intensification of drought stress, the AMF colonization rate of N. yunnanensis roots significantly decreased and changed both growth parameters, including leaf area, and photosynthetic characteristics, including net photosynthetic rate of N. yunnanensis seedlings. High AMF significantly enhanced N. yunnanensis tolerance to the imposed drought stress by improving both growth parameters and photosynthetic characteristics under conditions of adequate moisture and mild drought stress. Nevertheless, there were no significant differences between AMF treatments under severe drought stress, indicating that this had more significant effects on N. yunnanensis seedlings than did AMF. The results also demonstrated that the N. yunnanensis seedlings could not adapt to diverse water stress through plastic responses in morphology and photosynthesis, whereas high AMF treatments led to higher plastic differences in both growth parameters and photosynthetic characteristic. N. yunnanensis seedlings showed stronger drought resistance under high AMF conditions. The experimental results provide a theoretical basis for the scientific conservation and breeding of N. yunnanensis. In conclusion, N. yunnanensis seedlings did not show resistance to drought stress, but plants were dependent on mycorrhizae under water stress, which partially compensated its effects.