Drought serves as an important abiotic factor influencing plant growth and constraining agricultural progress. Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., a vital plant for afforestation and medicine in the deserts of northwestern China, frequently exhibits extensive root colonization by dark septate endophytes (DSE), while their precise role of DSEs in drought mitigation for A. mongolicus remains ambiguous. This study investigated the effects of DSE symbiosis (Gaeumannomyces hyphopodioides, Paraphoma radicina, and Magnaporthiopsis agrostidis) on the physiological and morphological changes in A. mongolicus leaves through a simulated water limitation experiment. Drought decreased shoot biomass by 20.94 %; however, all DSE strains mitigated this growth inhibition, particularly G. hyphopodioides, which enhanced biomass by 39.41 %. DSE inoculation further improved photosynthetic efficiency, leading to increases in chlorophyll content, net photosynthetic rate (Pn), and stomatal conductance (Gs). Additionally, DSE symbiosis elevated antioxidant enzyme activity and osmotic compound levels, thereby mitigating drought damage. Anatomical analysis showed that G. hyphopodioides-inoculated plants maintained superior leaf structure under drought, with ultrastructural studies confirming the stability of chloroplasts and mitochondria. Variation partitioning further confirmed that DSE symbiosis is a primary factor influencing plant growth and morphological changes. Overall, our study concludes that DSE inoculation, particularly with G. hyphopodioides, could enhance the growth of A.mongolicus under conditions of drought stress through the modulation of leaf morphology and physiology characteristics. These findings confirm that DSE symbiosis can enhance the yield and cultivation of A. mongolicus in arid regions, which is crucial for the its community restoration and resource utilization.