Dark septate endophytes (DSEs) are known to help host plants survive drought stress; however, how DSEs enhance host plant drought resistance under water stress conditions remains unclear. The objective of this study was to inoculate Ormosia hosiei seedlings with a DSE strain (Acrocalymma vagum) to investigate the effects of DSE inoculation on root morphology, ultrastructure, and the endogenous hormone content under drought stress conditions and to elucidate the drought resistance mechanism involved in the DSE–host-plant association. The inoculated seedlings were grown under three different soil water conditions (well watered—75% field water capacity, moderate water—55% field water capacity, or low water—35% field water capacity) for 114 days. Fresh root weight, root volume, root surface area, root fork, and root tip number were significantly higher in inoculated seedlings than in noninoculated seedlings. Furthermore, the root architecture of the inoculated seedlings changed from herringbone branching to dichotomous branching. Mitochondria and other organelles in root cells of inoculated seedlings remained largely undamaged under water stress, whereas organelles in root cells of noninoculated seedlings were severely damaged. The abscisic acid (ABA) and indole-3-acetic acid (IAA) content and IAA/ABA ratio of inoculated seedlings were significantly higher than those of noninoculated seedlings, whereas the content of gibberellic acid (GA) and the ratios of GA/ABA, zeatin riboside (ZR)/ABA, and ZR/IAA in inoculated seedlings were lower than those of noninoculated seedlings. DSE inoculation could help plants adapt to a drought stress environment by altering root morphology, reducing ultrastructural damage, and influencing the balance of endogenous hormones, which could be of great significance for the cultivation and preservation of the O. hosiei tree.