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Soil salinization poses a significant ecological and environmental challenge both in China and across the globe. Plant growth-promoting rhizobacteria (PGPR) enhance plants’ resilience against biotic and abiotic stresses, thereby playing a vital role in soil improvement and vegetation restoration efforts. PGPR assist plants in thriving under salt stress by modifying plant physiology, enhancing nutrient absorption, and synthesizing plant hormones. However, the mechanisms through which PGPR regulate the contents of carbon (C) and nitrogen (N), and biomass allocation of desert plant in response to salt stress is still unclear. This study explores the impact of PGPR on biomass allocation, C, and N contents of R. soongorica seedlings through a pot experiment. Strains P6, N20, and N21, identified as Enterobacter, were isolated from the rhizosphere of R. soongorica, and they exhibited various beneficial traits such as indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and tolerance to up to 8% NaCl stress. We found that under NaCl stress, R. soongorica seedlings exhibit significant reductions in plant height, basal diameter, and root surface area (P