Abstract: Organic fertilizer application is a primary farmland management strategy for enhancing soil microbial diversity and soil nutrient levels. However, the response mechanisms of soybean rhizosphere soil microbial community structure and basal respiration to organic fertilizer application require further exploration. This study, based on a 21-year long-term field experiment in Northeast China, examines the effects of different fertilization practices on soil nutrient stoichiometry, soil respiration, and microbial community structure. Results revealed that the C/N ratio of soybean rhizosphere soil under organic fertilizer treatment was significantly higher than that under no fertilizer (CK) and chemical fertilizer (NPK) treatments. Additionally, C/P and N/P ratios were significantly higher under organic fertilizer treatments compared to chemical fertilizer treatments. As organic fertilizer application rates increased, cumulative CO₂ emissions from soybean rhizosphere soil also rose. The high-rate organic fertilizer treatment (NPKO3) achieved 154.4 mg·kg⁻¹, which was 32.86% and 16.07% higher than the low-rate (NPKO1) and medium-rate (NPKO2) organic fertilizer treatments, respectively. The combined application of organic and chemical fertilizers significantly enhanced the diversity of rhizosphere soil microbial communities. Under NPKO3 treatment, the Shannon index of bacterial and fungal diversity was 12.57% and 15.83% higher than under NPK treatment, respectively. The dominant bacterial phyla in soybean rhizosphere soil were Proteobacteria and Actinobacteriota, while the dominant fungal phyla were Ascomycota and Basidiomycota. Notably, bacterial markers under NPKO3 and NPKO2 treatments and fungal markers were most abundant, comprising 66 and 13 species, respectively. Partial least squares path analysis indicated a significant positive correlation between soil microbial community diversity and cumulative soil CO₂ emissions. In conclusion, the combined application of organic and chemical fertilizers improves rhizosphere soil nutrients, microbial community diversity, and soil respiration, providing a theoretical basis for optimizing farmland management practices.