Background and aims <p>The combined application of tillage practice and organic materials significantly influences soil health and the sustainability of agricultural ecosystems; however, the intrinsic mechanism through which tillage depth interacts with the application depth of various types of organic materials, and thus influencing crop yield by regulating soil microbial communities and their functions, remains unclear.</p> Methods <p>Through a four-year field experiment, the effects of on soil bacterial communities, and soil quality index (SQI), and crop yield were investigated, namely, shallow ploughing at 15&#xa0;cm (T15), deep ploughing at 35&#xa0;cm (T35), shallow ploughing at 15&#xa0;cm integrated with shallow-soil straw return (T15 + S), deep ploughing at 35&#xa0;cm with deep-soil straw return (T35 + S), deep ploughing at 35&#xa0;cm with deep-soil organic fertilizer application (T35 + OM), and deep ploughing at 35&#xa0;cm with deep-soil straw return and deep soil organic fertilizer application (T35 + S + OM).</p> Results <p>The T35 + S, T35 + OM, and T35 + S + OM enhanced Proteobacteria and Actinobacteria while diminishing Acidobacteria, and facilitated the functional activities of carbon and nitrogen cycles within the soil bacterial communities. T35 + OM increased the complexity of the soil bacterial network, whereas T35 + S and T15 + S led to a reduction. The SQI of the four soil layers in the T35 + S, T35 + OM, and T35 + S + OM was increased by 0.84%–12.61%, 10.24%–11.91%, 8.10%–10.12% and 8.90%–15.25% compared to T15. The structural equation model indicates that the combined of tillage method and organic materials indirectly improved SQI and crop yield by enhancing soil structure, increasing nutrient availability and stimulating microbial community functions.</p> Conclusion <p>These findings suggest that deep ploughing combined with organic materials constituted an effective management strategy.</p>