Purpose The success of phytoremediation relies on beneficial plant-microbe interactions. However, the changes of soil microbiota, during the phytoremediation of ion-adsorption rare earth element (REE) mine tailings, are far fromunderstood. The present study was conducted to reveal the co-occurrence patterns and key regulating factors of bacterial communities in ion-adsorption REE mine tailings with phytoremediation. Materials and methods A field experiment was conducted on an ion-adsorption REE mine tailing to test three phytoremediation strategies: (i) phytostabilization with grasses, (ii) phytostabilization with economic crops, and (iii) phytoextraction with REE hyperaccumulators. The bacterial community diversity, co-occurrence patterns, and the key regulating environmental factors in bulk and rhizospheric soils after 16 months of reclamation were studied by 16S Illumina high-throughput sequencing. Results and discussion The soils of plots with REEs-hyperaccumulators had significantly higher α-diversity than those planted with non-accumulators. After phytoremediation, the diversity and relative abundances of bacteria assisting in nutrient acquisition pronouncedly increased in the bulk soil of the reclaimed plots. Some plant growth–promoting bacteria (PGPB), e.g., Rhodanobacter, Streptomyces, and Bacillus, were enriched in the rhizospheric soil samples. Meanwhile, soil nutrient (total carbon and total nitrogen) concentration and REE availability were the most significant factors shaping the bacterial communities. Furthermore, special bacterial consortia of Bacilli took up the positions of the keystone species. Conclusions The results revealed the co-occurrence patterns and key regulating factors of bacterial communities in ionadsorption REE mine tailings, which will provide more crucial information for the optimization of the reclamation of REE tailings.