Using plant growth-promoting rhizobacteria (PGPR) combined with hyperaccumulator is an ecologically viable way to remediate cadmium (Cd) pollution in agricultural soil. Despite recent advances in elucidating PGPR-enhanced phytoremediation, the response of plant-associated microbiota to PGPR remains unclear. Here, we found that the effective colonization of PGPR reshaped the rhizosphere nutrient microenvironment, especially driving the nitrogen cycle, primarily mediated by soil nitrate reductase (S-NR). Elevated S-NR activity mobilized amino acid metabolism and synthesis pathways in the rhizosphere, subsequently driving a shift in life history strategies of the rhizosphere microbiota, and enriching specific rare taxa. The reconstructed synthetic community (SynCom3) confirmed that the inclusion of two crucial collaborators (Lysobacter and Microbacterium) could efficiently foster the colonization of PGPR and aid PGPR in executing phytoremediation enhancement. Finally, the multi-omics analysis highlighted the critical roles of phenylpropanoid biosynthesis and tryptophan metabolism pathways in inducing SynCom3 reorganization and PGPR-enhanced phytoremediation. Our results underscore the significance of the rhizosphere microenvironment modification by PGPR for its colonization and efficacy, and highlight the collaborative role of rare microbiota in the context of PGPR-enhanced phytoremediation.