Background: Fungal endophytes can improve plant tolerance to abiotic stress, however, the role of these plant–fungal interactions in desert species ecology and their management implications remain unclear. This study aimed to assess whether dark septate endophytes (DSE) can shift the performance of Artemisia ordosica and associated soil microbial community under salt stress.Methods: We investigated the effects of three DSE (Alternaria chlamydosporigena [AC], Paraphoma chrysanthemicola [PC] and Bipolaris sorokiniana [BS]) isolated from desert habitats on plant morphology, physiology and rhizosphere soil microhabitat of Artemisia ordosica seedlings under different NaCl concentrations (0 %, 0.1 %, 0.2 %, and 0.3 %) in a growth chamber. Results: Three DSE strains could colonize the roots of A. ordosica, and the symbiotic response with host plants depended on DSE species and NaCl concentration. The greatest benefits associated with DSE occurred under 0.1 % NaCl. Specifically, AC improved root morphology, and increased total biomass and superoxide dismutase (SOD) activity; PC increased root morphology, root biomass, and glutathione (GSH) and indoleacetic acid (IAA) contents; and BS promoted SOD activity and GSH and IAA contents. DSE reduced the root Na+ content. Interestingly, BS promoted gram-positive (G +) and gram-negative (G −) bacteria under 0.1 % NaCl and the abundance of AM fungi under 0.2 % and 0.3 % NaCl. PC positively affected fungi, AM fungi, G − bacteria and actinomycetes under 0.2 % and 0.3 % NaCl, while AC increased the abundance of all examined microbes under 0.3 % NaCl. A structural equation modeling (SEM) demonstrated that DSE not only positively affects A. ordosica performance but also directly or indirectly impacts soil microbes by regulating the soil organic carbon (SOC), available phosphorus (AP), and alkaline nitrogen (AN) content.Conclusions: DSE isolated from A. ordosica enhanced the root development of host plants and altered the soil nutrient content and soil microbiota under different NaCl concentrations, possibly contributing to plant growth and ecological adaptability under saline environment. These results contribute to the understanding of the ecological function of DSE in desert ecosystems and may be used to promote vegetation restoration in salinized desert areas.