The enrichment of salt ions in saline soil can intensify the adsorption and precipitation of phosphate ions, resulting in the dual stress of ion toxicity and phosphorus deficiency on plants. Exploring and utilizing excellent phosphate-solubilizing bacteria (PSB) with salt tolerant characteristics from saline habitats is an effective approach to address plant phosphorus deficiency and salt stress damage in saline-alkali soils. This study utilized the highly efficient phosphate-solubilizing bacterium Serratia sp. AWH-NS6, isolated from the rhizosphere of Haloxylon ammodendron in saline desert habitats, as well as the constructed pqqE gene knockout mutant (related to organic acid secretion) and complementary strain to investigate the regulatory effects of pqqE gene mediated strain AWH-NS6 on the growth and salt tolerance of alfalfa (Medicago sativa) in saline-alkali soils from the Yellow River irrigation area of Ningxia via pot experiment. The results showed that the application of wild-type and complementation strain significantly improved the growth of alfalfa (plant height, root length and biomass) and enhanced nutrient uptake (nitrogen, phosphorus and potassium) compared to control treatment. Meanwhile, inoculation with wild-type, mutant and complementation strains significantly enhanced plant antioxidant enzyme activity (SOD, POD, CAT), reduced malondialdehyde content, increased proline and soluble sugar accumulation to alleviate oxidative stress. Furthermore, the application of strain AWH-NS6 significantly decreased soil pH and salt content, increased organic matter and available phosphorus content and enhanced soil enzyme activity. The structure and composition of soil microbial communities were changed by these three strains, with wild-type and complementary strains promoting soil nitrogen and phosphorus cycling, resulting in a significant enrichment of phosphate-solubilizing functional bacterial groups such as Gemmatimonadetes and Planctomycetes. The above indicated that the key phosphate-solubilizing gene pqqE mediates the ability of Serratia sp. AWH-NS6 to alleviate the toxic effects of salt stress on alfalfa, improved soil nutrient status and key enzyme activity, and enhanced the soil microenvironment by enriching beneficial microorganisms in the rhizosphere, thereby promoting the growth and salt tolerance of alfalfa.