Aims: This study evaluated the impact of wheat straw return and microbial agent application on rice field environments. Methods: Using Rice variety Chuankangyou 2115 and a microbial mix of Bacillus subtilis and Trichoderma harzianum. Five treatments were tested: T-1 (no straw return), T-2 (straw return), T-3, T-4, and T-5 (straw return with varying ratios of Bacillus subtilis and Trichoderma harzianum). Results: Results indicated significant improvements in rice root length, surface area, dry weight, soil nutrients, and enzyme activity across T-2-T-5 compared to T-1, enhancing yield by 3.81-26.63%. T-3 (50:50 microbial ratio) was optimal, further increasing root dry weight, soil enzyme activity, effective panicle and spikelet numbers, and yield. Dominant bacteria in T-3 included MBNT15, Defluviicoccus, Rokubacteriales, and Latescibacterota. Higher Trichoderma harzianum proportions (75% in T-5) increased straw decomposition but slightly inhibited root growth. Correlation analysis revealed a significant positive relationship between yield and soil microorganisms like Gemmatimonadota and Firmicutes at the heading stage. Factors like dry root weight, straw decomposition rate post-jointing stage, and elevated soil enzyme activity and nutrient content from tiller to jointing stage contributed to increased panicle and spikelet numbers, boosting yield. Conclusion: The optimal Bacillus subtilis and Trichoderma harzianum ratio for straw return was 50:50, effectively improving soil health and synergizing high rice yield with efficient straw utilization.