Purpose <p>The soil ecosystem of oasis wheat fields is fragile, and excessive use of synthetic fertilizers has contributed to soil degradation. Commercial organic fertilizers and green manure can reduce reliance on synthetic fertilizers in agricultural production. However, the effects of combining these practices on wheat growth and soil health remain unclear.</p> Methods <p>A 457-day in situ pot experiment involving spring wheat–soybean green manure–spring wheat rotations was conducted. Four treatments were applied during the wheat growing season: no fertilizer (CK), synthetic fertilizer providing N and P₂O₅ (CF), commercial organic fertilizer substituting 24% of N and P₂O₅ (OF), and reduced (24%) synthetic N and P₂O₅ fertilizers (RF). Wheat dry matter accumulation, nutrient uptake, soil bacterial and fungal community characteristics, and the soil health index (SHI) were assessed.</p> Results <p>The co-decomposition of commercial organic fertilizer and soybean green manure improved soil extracellular enzyme activity and increased soil nutrients. Compared with CF, the grain yield in 2022 considerably increased by 21.24%, whereas SHI increased by 40.72%. The α and β diversity of bacteria and fungi considerably decreased under the OF treatment. Metabolic and functional predictions revealed that OF increased the abundance of saprotrophic fungi and bacteria associated with carbohydrate and amino acid metabolism.</p> Conclusion <p>Optimized fertilization during the wheat season, combined with the return of soybean green manure, enhances soil health, boosts wheat growth, and improves nutrient uptake. These findings support sustainable agricultural development in oasis farmlands by integrating effective land use and fertilization strategies.</p>