Drought stress usually influences growth and secondary metabolite accumulation in the roots of Astragalus membranaceus var. mongholicus, resulting in varied qualities and medicinal properties. In this study, four different drought treatments (regular soil-water content[CK], mild drought stress[A1], medium drought stress[A2], and strong drought stress[A3]) were applied to evaluate the effects of drought on one-year-old Shanxi native A. membranaceus seedlings. The results showed that an increase in the growth of stems and leaves of A. membranaceus occurred 80-120 d following germination, and then it gradually decreased. A high accumulation of root biomass occurred during the withering period of the aboveground parts of the plants. Drought stress reduced the height and aboveground biomass significantly and affected antioxidant activity, root development, and secondary metabolite accumulation. Under A1 conditions, the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), were raised with increased root length, root biomass, polysaccharides, and saponins. However, the malondialdehyde (MDA) content and cell membrane permeability decreased accompanied with a significant improvement in the overall quality of A. membranaceus (P < 0.05). The SOD activity decreased, and it was lower than that of the control under the A4 conditions. For increased drought stress, the activities of POD and CAT, MDA content, and cell membrane permeability were all increased and consequently resulted in a decreasing in root length, root biomass polysaccharides, saponins and the overall quality of the plant (P < 0.01). In summary, the result showed that the SOD activity was more sensitive to drought stress, suggesting a major function in the resistance to active oxygen. In addition, mild drought stress might promote the interaction between the antioxidant enzyme system and secondary metabolism system in A. membranaceus by increasing resistance to cell damage. The quality and yield of root could be improved by reducing aboveground growth for nutrient transportation to roots to some extent. The results of this study can be applied to promote the production of A. membranaceus with high polysaccharide and saponin contents through water management.