The Xinjiang mining area faces a severe soil salinization problem that restricts plant growth. Addressing saline-alkali soil is crucial for ecological restoration in the mining area. Dark septate endophytes (DSE) can enhance plant stress resistance and are important for ecosystem restoration and promoting vegetation restoration. The DSE in the roots of the dominant plant Suaeda salsa in unmined areas, vegetation reclamation areas, and undisturbed area without reclamation around the Hongshaquan saline-alkali mining area in Xinjiang are investigated. DSE micromorphology and physiological and biochemical responses under varying NaCl concentrations, and the salt tolerance characteristics of plant root symbiotic DSE are explored, aiming at providing a theoretical basis for ecological restoration in this region. The study found that S. salsa from different sampling sites in the area could form a favorable symbiotic relationship with DSE, and 23 DSE strains were isolated from S. salsa roots. Following initial screening for salt tolerance, four strains were selected. Among these, Chaetomium globosum maintained growth under 3 mol/L NaCl stress, exhibiting significantly superior biomass, reduced glutathione content, and sporulation capacity compared to the other strains. The remaining three Alternaria spp. strains displayed distinct microstructural alterations under 2 mol/L NaCl salt stress, including a significant increase in mycelium diameter, shortened septum spacing, and a wrinkled surface. This structural differentiation may represent their adaptive response to salt stress. Furthermore, these three DSE strains mitigated salt stress damage through physiological mechanisms such as increasing soluble protein content and enhancing superoxide dismutase (SOD) and catalase (CAT) activities. The results provide a theoretical basis for screening salt-tolerant microorganisms and applying microbial reclamation technology in saline-alkali mining areas in Xinjiang.