Dark septate endophytes (DSEs) are a type of endophytic fungus that commonly colonize plant root systems in extreme environments, and play a role in enhancing resistance to drought stress. To investigate the potential applications of DSEs in improving drought tolerance of desert plants, three DSE strains isolated from Haloxylon ammodendron for strong drought tolerance - Alternaria tellustris (AT), Cladosporium sp. (CL), and Paraphoma radicina (PR) - were screened through pure culture in vitro. Pot experiments of H. ammodendron were then conducted with different DSE, water, and soil treatments. In both sterilized and nonsterilized soil, DSEs showed growth-promoting and drought-resistant properties, with a stronger effect observed under sterilized soil treatment. The results showed that in sterilized soil, AT and CL increased root biomass, total biomass and root shoot ratio under high drought treatment, while PR effectively enhanced branch number and root biomass under normal water treatment. Physiologically, DSEs improved plant drought tolerance by increasing soluble sugar content and superoxide dismutase activity. Notably, DSE inoculation facilitated the uptake and utilization of soil nutrients such as available phosphorus, nitrate nitrogen, and free amino acids by plants in both sterilized and nonsterilized soil. Overall, our study highlights the potential of DSEs in improving drought resistance and promoting the growth of desert plants.