In order to explore the effect of microbial fertilizer on saline-alkali soil under water-saving irrigation, a field experiment on sunflowers was carried out in Hetao Irrigation District. Different combination of irrigation gradients (0%, 10%, 20% water-saving condition) and ETS microbial fertilizer (Thomas microbiota and Pasteurella microbiota) application gradients (0; 3,000; 4,500 kg/hm2) were established to examine the impact of microbial fertilizer treatments on soil physicochemical properties, microbial community structure, and sunflower growth under different water-saving irrigation conditions. The results show that for the application of 4,500 kg/hm2 solid microbial fertilizer and 180 L/hm2 liquid microbial fertilizer, 20% water-saving condition significantly reduced the soil bulk density and pH, significantly increased the soil moisture content, total porosity, as well as the contents of organic matter, total nitrogen, available phosphorus, and available potassium (P<0.05), compared with 0% water-saving condition. The stem diameter and sunflower yield were also improved (P<0.05); whereas the stem height and disc diameter showed no significant change (P>0.05). Proteobacteria, Cyanobacteria, Gemmatimonadota, Actinobacteriota and Acidobacteriota were the dominant phyla in the saline-alkali soil in Hetao Irrigation District, with Chloroplast, and S0134_terrestrial_group as the dominant genera. Soil moisture content showed a significant negative correlation with Actinobacteriota (P<0.05); organic matter showed a significant positive correlation with Gemmatimonadota, Planctomycetota, and S0134_terrestrial_group, and a significant negative correlation with Firmicutes (P<0.05); soil total nitrogen showed a significant positive correlation with Gemmatimonadota, Acidobacteriota, Chloroflexi, Myxococcota, NB1-j, and Rokubacteriales (P<0.05). The application of microbial fertilizer under water-saving irrigation is conducive to water saving, soil improvement and the efficient utilization of water and fertilizer in sunflower.