Background and aims <p>Straw incorporation (SI) is a widely adopted management strategy that improves soil fertility, alters soil-microbe-plant interactions, and enhances crop yield in agroecosystems. A deep understanding of soil-microbe-plant interactions in response to SI is crucial for optimizing fertilization practices and boosting crop yield; however, relevant knowledge remains limited.</p> Methods <p>A two-year consecutive field experiment was conducted during winter wheat growing seasons to investigate the effects of fertilization at the level of 0&#xa0;kg N ha^–1 (N0) and 210&#xa0;kg N ha^–1 (N1) under straw incorporated (S1) and removal (S0) on soil environment, microbial community structure and plant growth and yield.</p> Results <p>SI had a significant effect on soil organic matter (SOM) content, while fertilization had a significant effect on NO₃^– concentration, SOM and TN contents. N1S1 decreased the root length and total surface area (TSA), but increased aboveground biomass and yield by 32.7% (P &lt; 0.05) and 2.6%–4.1%, respectively, as compared to N1S0. Additionally, crop yield showed a highly significant correlation with SOM. N fertilization reduced bacterial and fungal diversity, while SI significantly altered the composition and increased bacterial and fungal diversity. Structural equation modelling revealed that the increases of soil moisture and SOM content induced by SI could directly enhance the interaction among root growth, leaf area index, and bacterial communities, thereby improving crop yield.</p> Conclusion <p>SI can offset the negative impacts of N fertilization on soil microbial community structure by regulating soil SOM content and plant growth, and can modulate winter wheat yield through mediating plant–soil–microbe interactions.</p> Graphical Abstract <p></p>