Introduction Soybean cultivation in southern Xinjiang of China is constrained by multiple natural and anthropogenic factors. This study explored the synergistic effects of microbial inoculation and planting density on summer-sown soybeans to find the optimal solution for high and stable yield.Methods Herein, A two-year field experiment was conducted with a split-plot design. Four planting densities were applied in the main plots: 123, 000 plants hm-2 (D1); 82, 000 plants hm-2 (D2); 59, 000 plants hm-2 (D3); and 44, 000 plants hm-2 (D4) . In the subplots, eight inoculation treatments were established: no inoculation (C0, control); single inoculation with Bacillus (T0); co-inoculation with Bacillus and Rhizobium fredii SMH12 (T1), Bacillus and Rhizobium fredii SN7-2 (T2), Bacillus and and Rhizobium fredii HN01 (T3); and single inoculation with Rhizobium fredii SMH12 (T4), Rhizobium fredii SN7-2 (T5), and Rhizobium fredii HN01 (T6).Results The results showed that microbial inoculation and planting density significantly affected plant growth, root nodulation, nutrient accumulation, and yield. T2 resulted in the highest yield under the D3 density (5174 .59-5385. 67 kg hm-2), which was improved by 7 .8 -69.9% over that of other treatments. This yield improvement was achieved mainly through increasing seed number per plant and 100-seed weight without reducing pod number per plant. The increase in 100-seed weight was related to higher root nodulation potential and nutrient accumulation level. The D3 density optimized plant morphology (especially in increasing main-stem node number and stem diameter), thereby contributing to higher yield. Correlation analysis showed that yield was highly positively correlated with main-stem node number and root nitrogen accumulation. Principal component analysis identified D3T2 as the largest contributor to plant growth (comprehensive score F = 1 . 28).Conclusion Overall, These findings suggest that co-inoculation with Bacillus and Rhizobium SN7-2 under a planting density of 59, 000 plants hm-2 is suitable for high-yield cultivation of summer-sown soybeans under the experimental conditions. This study provides an effective agronomic strategy for enhancing soybean yield potential and stress resistance in arid regions with poor soil fertility.