Dark septate endophytes (DSEs) are a type of endophytic fungi colonizing plant roots with a broad distribution, especially in extreme habitats such as deserts. Various studies have demonstrated that DSEs can enhance plant growth under stress conditions. In this study, wheat seedlings were inoculated with two desert-derived dark septate endophytes, Alternaria alstroemeriae (Aa), Paraphoma chrysanthemicola (Pc), or left uninoculated as control (CK), and exposed to either adequate watering (WW) or drought (DD) conditions. Six treatment groups, Aa_WW, Aa_DD, Pc_WW, Pc_DD, CK_WW and CK_DD, were established. The results suggested that inoculation with either Aa or Pc significantly promoted wheat performance under WW and DD conditions. Under two water conditions, inoculation with Aa and Pc significantly promoted the shoot and root growth of wheat. Notably, Aa exhibited a stronger promoting effect on root system under DD treatment, increasing total root length by 17.75%. Under DD treatment, inoculation with Pc significantly enhanced wheat photosynthesis, increasing photosynthesis rate, stomatal conductance, transpiration rate, and chlorophyll content by 30.00%, 33.33%, 47.22%, and 5.61%, respectively. Both DSE strains enhanced osmotic adjustment under drought stress. Aa increased soluble sugar, soluble protein and glutathione contents, while Pc elevated proline and glutathione levels, leading to significant reductions in malondialdehyde accumulation by 24.24% and 19.09%, respectively. In addition, both Aa and Pc significantly increased auxin content of wheat leaves. Consistent with the improved physiological and growth performance, transcriptomic analysis revealed that DSE inoculation induced differential expression of genes primarily enriched in pathways related to photosynthesis, carbohydrate metabolism, signal transduction, antioxidants defense, collectively contributing to enhanced wheat drought tolerance. Consequently, these findings demonstrate the great potential of desert-derived DSE strains for improving wheat growth and drought resilience in arid and semi-arid agricultural ecosystems.