This study investigated the effects of Bacillales bacteria on the growth phenotype and gene expression of Arabidopsis thaliana. Seven bacterial strains isolated from the rhizosphere of wild Arabidopsis were tested through single inoculation and co-inoculation experiments. The results showed that certain strains (such as Root 147, Root 444D2, and Root 239) significantly inhibited primary root elongation while promoting increased root hair density and length, exhibiting the characteristic “Bacillus effect.” In co-inoculation experiments, both synthetic communities F1 and F2 markedly altered root morphology. Among them, F1 exerted stronger inhibitory effects under high nutrient conditions, whereas F2 showed more pronounced effects under low-nutrient and nitrogen limited environments. Transcriptomic analysis revealed that F1 inoculation upregulated genes related to nutrient transport and cell wall modification in roots, while genes associated with defense and circadian rhythm were predominant in shoots. Overall, Bacillales bacteria modulate plant growth and gene expression through multiple regulatory layers, demonstrating their potential as plant growth promoting bacteria (PGPB) and providing new insights into microbe-mediated plant growth promotion.