Beneficial microorganisms are an effective approach to ameliorate degraded soils and improve farmland productivity. At present, systematic research on the regulatory effects of plant growth-promoting bacteria on tomato growth in acidic soils is still lacking. In this study, pot experiments combined with microbiome technology were conducted to investigate the effects of Bacillus cereus BC-101, Bacillus methylotrophicus BM-25 and Bacillus amyloliquefaciens BA-11 on the growth of tomato seedlings and the structure of rhizosphere microbial communities in acidic soils. All the three tested plant growth-promoting bacteria significantly promoted the growth of tomato seedlings. The plant heights were increased by 43.01%, 94.38% and 99.20% under BC, BM and BA treatments, respectively. Meanwhile, the bacterial inoculation significantly increased plant biomass, improved leaf photosynthetic pigment contents, activated protective enzyme activities, and elevated the contents of osmotic adjustment substances and growth-promoting hormones. In addition, the bacteria could improve the physicochemical properties of acidic soils, enhance soil enzyme activities, and significantly increase the relative abundances of beneficial genera such as Pseudomonas and Bacillus in the rhizosphere. Rhizospheric inoculation of the three plant growth-promoting bacteria improved tomato growth and enhanced rhizosphere soil properties under naturally acidic soil conditions, suggesting their potential application in the biological improvement of acidic soils. This study provides practical evidence for the comprehensive improvement and application of acidic soils.