Abstract: Long-term straw return is a crucial agronomic practice for improving soil fertility and sustaining high and stable grain yields. While numerous studies have investigated the response characteristics of soil microbial community composition and diversity to straw return, the relationships between microbial community-level functional attributes, network characteristics, and grain yields remain unclear. On the basis of a 28-year field experiment with three treatments—no fertilization (NF), chemical fertilization (CF), and chemical fertilization combined with straw return (CFS) — this study systematically analyzed the effects of long-term straw return on microbial community functionality, potential interspecific interactions, and their contributions to the maize yield. The results showed that compared with NF, both CF and CFS significantly increased the maize yield by 58.72%–217.52%, with no significant difference between the two fertilization treatments. In terms of soil quality improvement, both CF and CFS increased soil organic carbon and nutrient content, and CFS showed more pronounced improvement effect, effectively alleviating soil acidification caused by single chemical fertilization. The functional annotation results showed that fertilization significantly altered microbial community-level functional composition. The CFS treatment had the highest functional redundancy of microbial communities, with higher relative abundance of chemoheterotrophic, lignin-degrading, and cellulose-degrading groups than other treatments. Co-occurrence network analysis further revealed that long-term straw return reshaped microbial interaction relationships, with the CFS treatment exhibiting the highest network complexity. This increase in complexity was mainly attributed to the enrichment of Proteobacteria and Bacteroidetes, as well as the enhancement of nutrient cycling-related functional modules. Joint analysis using random forest and structural equation models showed that compared with microbial community composition, functional gene composition, and soil physicochemical properties, microbial community network complexity was the core factor driving crop yield variations. In conclusion, long-term straw return enhances the stability and resilience of agroecosystems by increasing soil nutrient storage capacity, promoting the development of functional microbial groups, and constructing complex microbial interaction networks, serving as an important approach for achieving soil health improvement and sustainable development of crop productivity. This study reveals the key role of microbial community network complexity in maintaining stable crop yields and provides a new theoretical basis and mechanism framework for optimizing soil management practices in intensive farmlands as well as ensuring food security and agricultural environmental sustainability.