Abstract: To elucidate the microbial mechanisms underlying the improvement of saline-alkali soil by organic fertilizer, this study took the saline-alkali soil in the wheat-growing area of the Nanpi Ecological Agriculture Experimental Station of the Chinese Academy of Sciences as the research object. Through a four-year field positioning experiment and by combining with metagenomic sequencing, it comparatively analyzed the structural and functional characteristics of soil microbial communities under organic fertilizer （OF） and equivalent chemical fertilizer （CK） treatments. Soil physicochemical analysis revealed that OF treatment significantly enhanced soil nutrient content （total nitrogen, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium） and alkaline phosphatase activity （P <0.05）. Microbial diversity analysis showed that OF treatment significantly increased community richness and altered community structure, as confirmed by β-diversity analysis. Among the top 10 dominant genera, the relative abundances of Acidobacterium and Luteitalea significantly increased, while those of Solirubrobacter, Gaiella, and Steroidobacter significantly decreased. Co-occurrence network of soil microbial communities further revealed that OF treatment enhanced microbial interaction complexity （with a 33.9% increase in node numbers） and modularity （exhibiting a 2.23-fold rise in module count）. Functional annotation results indicated that OF treatment exhibited significant enrichment in 8 pathways, including sphingolipid metabolism, ribosome biogenesis, and lipopolysaccharide biosynthesis, whereas CK treatment was primarily enriched in 4 pathways, such as RNA polymerase and proteasome. In conclusion, organic fertilizer synergistically improves the ecological functions of saline-alkali soils by improving soil physicochemical properties and regulating microbial community structure, strengthening microbial interactions, and optimizing metabolic functional networks, thereby providing theoretical support for the biological remediation of saline-alkali soils.