Dark septate endophytes (DSE) commonly inhabit the root systems of plants that flourish in heavy metal-contaminated soils. Nevertheless, there is limited understanding regarding the overall response of medicinal plants to DSE under heavy metal stress. The present study utilized a non-sterile pot experiment to evaluate the beneficial impacts of DSE (Paraphoma chlamydocopiosa, Paraboeremia selaginellae, and Paraphoma radicina) inoculation on Astragalus mongholicus under cadmium (Cd) stress. At 0 mg Cd/kg soil, inoculation with DSE led to a significant increase in the total biomass of the host plant by up to 34.0%. Although plant biomass decreased at 5 mg Cd/kg soil and 10 mg Cd/kg soil, the total biomass of the host plant increased by up to 72.3% after DSE inoculation. The plant height, branch number, soil and plant analyzer development (SPAD) value, and biomass were not affected by Cd concentration after inoculation with P. chlamydocopiosa and P. selaginellae. DSE emerged as the most prominent explanatory variable (44.2%) for plant growth at 10 mg Cd/kg soil. Inoculation with P. chlamydocopiosa increased root length by 47.9% and root biomass by 74.1%, and inoculation with P. chlamydocopiosa and P. selaginellae increased the indole-3-acetic acid (IAA) content by 103.6% and 105.8%, respectively, at 10 mg Cd/kg soil. Additionally, P. radicina inoculation was preferred to increase the content of calycosin-7-O-glucoside, while P. chlamydocopiosa increased the content of formononetin. DSE enhanced the accumulation of Cd in the shoot, whereas P. radicina exhibited an inhibitory effect on Cd accumulation in the root system. P. chlamydocopiosa decreased the Cd translocation factor, while P. radicina increased the Cd translocation factor, which exceeded one. The interaction between DSE and soil factors significantly contributed to the host plant growth. DSE inoculation improved soil organic carbon content and inoculation with P. chlamydocopiosa, and P. selaginellae reduced available nitrogen content, regardless of the Cd stress. DSE inoculation reduced available phosphorus content at 10 mg Cd/kg soil. Importantly, P. radicina promote the performance and calycosin-7-O-glucoside accumulation of the host plant, and reduced Cd content in the roots at 5 mg Cd/kg soil. These data enhanced comprehension of the ecological function of DSE in heavy metal-contaminated soils and demonstrated the potential utility of DSE strains for cultivating medicinal plants.