【Objective】This study aimed to investigate the synergistic effects of different water and fertilizer treatments on the physicochemical properties, bacterial community structure, and ion transport function of saline-alkali maize fields, thereby providing a theoretical basis for their targeted improvement. 【Method】A field experiment was conducted in saline-alkaline land in Pingluo County, Ningxia. A split-plot design was used with two irrigation levels as main plots: conventional irrigation (w1, 6 000 m3hm-2) and water-saving irrigation (w2, 4 800 m3hm-2)， and four fertilization modes as sub-plots: f1 (nitrogen fertilizer alone), f2 (nitrogen with controlled-release fertilizer), f3 (nitrogen with organic fertilizer), and f4 (controlled-release fertilizer with organic fertilizer). Soil physicochemical properties were measured. Bacterial community structure was analyzed by 16S rRNA high-throughput sequencing, and the abundance of ion transporter genes was predicted using PICRUSt2 software. 【Result】Water-saving irrigation w2 exhibits no significant difference in its impact on soil physicochemical properties compared to conventional irrigation w1. Compared with w2f1 treatment, the w2f3 treatment significantly increased the contents of soil organic matter (SOM), total nitrogen, alkaline hydrolyzable nitrogen, available phosphorus, available potassium, and Ca2+ (P<0.05), while significantly decreasing pH, electrical conductivity, and Na+ content (P<0.05). The water-fertilizer interaction had highly significant effects on the contents of sodium, magnesium, potassium, and calcium ions (P<0.01). Microbial analysis showed that the w2f4 treatment significantly increased the Simpson diversity index and Pielou evenness index (P<0.05). At the phylum level, w2f3 and w2f4 significantly increased the relative abundance of Proteobacteria and Actinobacteria, while decreasing the relative abundance of Acidobacteria (P<0.05). At the genus level, Kaistobacter and Lysobacter were the dominant genera, and their abundance was significantly increased by the w2f3 treatment (P<0.05). Linear discriminant analysis effect size analysis identified 32 biomarker species across five phyla, with w2f3 significantly enriching Proteobacteria and Bacteroidota. Prediction of ion transporter genes indicated that the w2f3 treatment simultaneously activated the magnesium transporter gene CorA and the Na+/H+ antiporter gene nhaA. The ecological dominance of Proteobacteria was positively regulated by KefB and CorA. Mantel test confirmed that SOM and pH were the core environmental factors driving the evolution of the microbial community structure.【Conclusion】Under water-saving irrigation, the combined application of nitrogen fertilisers with organic fertilisers (w2f3) achieves systematic restoration of ecological functions in saline-alkali soils by synergistically enhancing soil fertility, optimising bacterial community structures, and activating ion homeostasis networks. This provides both theoretical and technical underpinnings for the efficient remediation of saline-alkali land.