To evaluate the effects of brackish-water deficit irrigation combined with microbial fertilizer on soil salinization, microbial community structure, and predicted functions, a field experiment was conducted on moderately saline-alkaline soils in the Hetao Irrigation District using Lycium barbarum as the indicator crop. Brackish water irrigation depths were set under microbial fertilizer application (W1: 180mm, W2: 240mm, W3: 300mm, CK: 330mm). It was found that, compared with CK, total soil salinity under W2 was reduced by 56.77% from the fruit expansion to defoliation stages, and Na⁺ was reduced by 55.87% (excluding the flowering stage). During critical yield-formation stages, K⁺, Ca²⁺ and Mg²⁺ were decreased by 45.29%~78.28%. The sodium adsorption ratio (SAR) was decreased by 33.65% and 54.23% at the fruit expansion and leaf drop stages, respectively. In early growth stage, soil pH was increased by 3.63% under W1(P<0.05), whereas no significant differences among treatments were detected thereafter (P>0.05). The bacterial community was dominated by Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria, with Sphingomonas and Pseudomonas as predominant genera. Under W2, the relative abundance of Acidobacteria was increased by 28.09% (P<0.05), and during the fruit expansion stage the relative abundance of Sphingomonas was significantly higher than under CK; this genus was significantly negatively with Cl^- content (P<0.05) and SAR value (P<0.01). Under brackish water irrigation, Bacillus amyloliquefaciens was selectively enriched under W2 (57.6% relative to CK; P<0.05), and accumulation of Paenibacillus mucilaginosus at the peak fruiting stage was promoted; enrichment of both taxa was maintained through defoliation.Functional prediction indicated that chemoheterotrophy and aerobic chemoheterotrophy were the primary community functions, and the abundances of carbon- and nitrogen-cycling functional groups were increased by 8.25% and 36.31%, respectively, under deficit brackish-water irrigation. Redundancy analysis (RDA) indicated that K⁺, Mg²⁺, Cl^-, and Na⁺ were the key drivers of microbial community variation, with a cumulative explanatory rate of 54.65%. The soil quality index (SQI) based on principal component analysis (PCA) indicated stage-dependent irrigation demand: at the flowering stage, W3increased SQI by 14.46%, whereas from the fruit expansion to defoliation, SQI under the W2 increased by 381.11%. On the basis of the SQI-irrigation volume model, an optimal brackish-water irrigation depth of 240~260mm under microbial fertilizer application was proposed.