To investigate the regulatory effects of microbial fertilizer under brackish water irrigation on soil water-salt dynamics and Lycium barbarum yield in moderate salt-affected soils, and to develop a brackish water-microbial fertilizer co-management strategy suitable for the Hetao Irrigation District, a field experiment was conducted using Ningqi No.9 as the test crop, four microbial fertilizer application rates were designed: CK (0 kg/hm²), F1 (45 kg/hm²), F2 (75 kg/hm²), and F3 (105 kg/hm²). The results showed that microbial fertilizer significantly improved soil moisture. During peak fruiting stage in summer, F3 reached the highest water content in the 0-40 cm layer (29.34%), which was 25.81% higher than CK. Additionally, water storage in the 0-60 cm root zone increased by 31.93%. Microbial fertilizer reduced soil salinity across all depths. Specifically, F3 decreased total salt content in the 0-20 cm surface layer by 54.22%, while F2 reduced salt in the 20-100 cm mid-deep layer by an average of 40.18%. Both F1 and F2 showed strong salt regulation across the 0-100 cm profile. They achieved early-stage salt removal of 23.15% and 21.82%, respectively, and maintained lower late-stage salt accumulation (33.22% and 32.78%). Yield followed a unimodal response, with F2 increasing yield by 46.33% compared to CK. Under F3, the fruit’s longitudinal and transverse diameters increased by 30.05% and 10.20%, respectively, resulting in a significant increase of 17.93% in the shape index. In contrast, F2 promoted more balanced growth, with transverse and longitudinal diameters increasing by 1.29% and 9.29%, respectively, leading to a 8.15% increase in the fruit shape index. Partial least squares path modeling (PLS-PM) indicated that microbial fertilizer indirectly influenced yield by modulating soil water storage, with opposing effects on fruit dimensions: enhancing longitudinal diameter while suppressing transverse growth. Considering both soil water-salt regulation and yield response, the application rate of 69-76 kg/hm² of microbial fertilizer is recommended to balance desalination, water retention, and yield improvement in this study area.