Abstract: To investigate the synergistic effects of straw returning patterns combined with decomposition-promoting microbial agents on soil nutrients and microbial communities, this study established four treatments: conventional straw returning (SR), straw returning with microbial agents (SRM), straw returning with vertical deep rotary tillage (SRVT) and straw returning with vertical deep rotary tillage plus microbial agents (SRVTM). The structural characteristics of soil bacterial communities were analyzed using high-throughput sequencing technology, and the interactions between microbial communities and nutrient factors were elucidated through soil nutrient analysis. Results showed that compared with SR treatment, although SRVT increased total nitrogen (TN) and available phosphorus (AP) by 2.8% and 42.4% respectively, it reduced organic matter (OM), alkaline hydrolyzable nitrogen (AN) and available potassium (AK), while exhibiting the lowest daily organic carbon mineralization rate and cumulative mineralization among all treatments. SRM treatment significantly enhanced AN, AP and AK contents (increased by 5.4%, 154.9% and 5.0%, respectively) and promoted microbial activity. The SRVTM treatment demonstrated comprehensive advantages: OM, total phosphorus (TP), AN, AP and AK increased by 3.8%, 11.6%, 9.8%, 133.1% and 27.9% respectively compared to SR, with the highest daily organic carbon mineralization rate on the first day and maximum cumulative mineralized organic carbon over 30 days. It also showed a 41.9% increase in specific microbial populations, the highest number of differential species among the top 30 abundant taxa, and elevated relative abundances of Proteobacteria and Acidobacteriota by 2.63% and 0.45%, indicating optimized ecological functions through enhanced carbon-nitrogen cycling functional microbiota. Further analysis revealed that soil N, P and K contents were primary drivers of microbial community structural variation. In conclusion, while single vertical deep rotary tillage showed limited effects on soil nutrient improvement, its combination with straw-decomposing microbial agents activated microbe-nutrient synergism, providing an optimized strategy for soil carbon sequestration and fertility enhancement in rice-wheat rotation systems.