Phytoremediation of soils contaminated with high concentrations of multiple heavy metals (HCMHMs) is a promising technique. However, the microbial response mechanisms during the phytoremediation process remain poorly understood. The role of microbes in HCMHMs soil remediation may be underestimated. This study investigated microbial responses and their potential roles in HCMHMs soil remediation using the hyperaccumulator plant Sedum alfredii (S. alfredii). Soil microbial communities were characterised by 16S rRNA sequencing, and metabolic pathways and functions were predicted using PICRUSt2 analysis. The results indicated that the impact of heavy metals on bacterial community structure was more significant than that of S. alfredii. The formation of dominant phyla such as Proteobacteria and Patescibacteria played a crucial role in the bacterial remediation of HCMHMs soils. Proteobacteria utilised the Inorganic ion transport and metabolism gene clusters to translocate heavy metals or reduce their bioavailability and toxicity. Patescibacteria used the Replication, recombination and repair gene clusters to repair damaged genes, enhancing bacterial tolerance of heavy metals. The results provided new insights into the role of microbes during phytoremediation and offered a scientific basis for optimizing phytoremediation technologies. This study demonstrated that dominant phyla effectively mitigated the damage to soil ecological functions from HCMHMs soil.