Abstract: Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrient content and promote plant growth and health. However, the growth-promoting effects of a single PGPR on plants are limited. To explore the effects of synthetic microbial communities on soybean growth, rhizosphere, and endophytic microbiota, soybean PGPR was used to construct four synthetic microbial communities (SynComs) based on functional complementarity and efficacy stacking principles. The optimal community was chosen for its growth-promoting effects, and metagenomic sequencing was performed on its rhizosphere soil, while roots underwent 16S rRNA gene sequencing. This aimed to investigate the microbial community structure and functional changes of bacteria in both the soybean rhizosphere and endosphere. Pot experiments showed that SynCom 4 significantly increased soybean plant height, aboveground fresh weight, root length, root fresh weight, and nodule number. SynCom 4 comprised Klebsiella JP07, Klebsiella GD04, Pseudomonas LH19, Acinetobacter JP32, Klebsiella PKO08, Bacillus JK32, Stenotrophomonas GD03, and Klebsiella LH13. Principal component and community composition analyses were performed using the metagenomic sequencing data, uncovering significant changes in the rhizosphere microbial community structure after treatment with SynCom 4. Ten major phyla, including Proteobacteria, Firmicutes, and Actinobacteria, were identified at the phylum level. LEfSe analysis indicated an increase in the relative abundance of taxa such as unclassified_Acidimicrobiia, Luteimonas, unclassified_c_Chloroflexia, and unclassified_o_Thermoanaerobacteroles in SynCom 4. Introducing SynCom 4 increased the relative abundance of functional genes associated with nitrogen metabolism, phosphorus transformation, and indole acetic acid, and gibberellin biosynthesis. According to 16S rRNA gene sequencing results, community composition analysis revealed that the dominant bacterial phyla in the endosphere included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Inoculation with SynCom 4 increased the diversity of the soybean endosphere bacterial community. LEfSe analysis demonstrated an increase in the relative abundance of taxa such as unclassified_f_Xanthomonadaceace, Hydrogenophaga, unclassified_o_Rhizobiales, and norank_f_Xanthobacteraceae following the application of SynCom 4. PICRUSt2 functional predictions indicated that SynCom 4 enhanced functions related to synthesizing amino acids, vitamins, lipids, and secondary metabolites. In summary, metagenomic and 16S rRNA gene sequencing results indicated that SynCom 4 significantly altered the structure and composition of the rhizosphere and endosphere microbial communities. This intervention led to increased microbial diversity and an elevated relative abundance of microbes. The application of SynCom 4 effectively promoted soybean growth and changed the structure and function of the bacterial microbial community in the rhizosphere and endosphere.