Purpose This study aimed to isolate plant growth-promoting rhizobacteria (PGPR) that exhibit heavy metal resistance to examine their influence on Cd uptake and soil microbial community structure during phytoremediation. Materials and methods Heavy metal-tolerant PGPR were isolated from the roots of possible hyperaccumulators using plates with 1-aminocyclopropane-1-carboxylate (ACC) as sole nitrogen source. Minimal inhibitory concentrations (MICs) of each isolate were determined by the plate dilution method. The impacts of isolated PGPR on the growth and Cd accumulation of Sedium plumbizincicola were conducted in a pot experiment. In addition, the effect of PGPR inoculation on the microbial community during phytoextraction by S. plumbizincicola was studied by 454 pyrosequencing. Results and discussion A total of nine Cd-resistant strains were isolated from the roots of Cd accumulators, and their plant growth-promoting activities were characterized. Isolates were able to produce indole-3-acetic acid (IAA) (28-133 mg L − 1 ) and solubilize phosphate (65-). In a pot experiment, the inoculation of isolates NSX2 and LCR1 significantly enhanced the growth of and u p t a k e o f C d b y t h e C d h y p e r a c c u m u l a t o r S. plumbizincicola. 454 pyrosequencing revealed that the inoculation of the PGPR lead to a decrease in microbial community diversity in the rhizopshere during phytoextraction. Specifically, indigenous heavy metal-tolerant PGPR such as Actinospica, Bradyrhizobium, Rhizobium, Mesorhizobium, and Mycobacterium were selectively enriched in the treatments in which PGPR were added. It is suggested that a unique constitution of microbial communities in inoculated t r e a t m e n t s p l a y s a k e y r o l e i n e n h a n c i n g C d phytoremediation. Conclusion Inoculation of strains Rhodococcus erythropolis NSX2 and Cedecea davisae LCR1 could promote S. plumbizincicola growth and enhance the remediation efficiency. The introduced PGPR could also affect the indigenous microbial community structure and the diversity in Cdcontaminated soil during phytoremediation.