Introducing hyperaccumulators in bamboo forests is an efficient method for heavy metals (HMs) pollution control. HMs can be transferred from soil to bamboo and accumulate in edible bamboo shoots. However, how phytoremediation or cropping systems affect root‐soil interface and transference of HMs from soil to bamboo shoots is unknown. In this study, lei bamboo and Sedum plumbizincicola were planted as a monoculture and intercropping system (bamboo/sedum) on contaminated land. Soil properties, rhizosphere bacterial communities, and HMs concentrations in plants and soils were compared among bamboo in monoculture (B), bamboo in intercropping (BI), sedum in intercropping (SI), and sedum in monoculture (S). In BI, the total nitrogen was 10.8% lower, while total organic carbon (TOC) was 12.3% higher than in B; HMs removal amount in BI was higher than in B, especially cadmium. Intercropping increased the HMs concentrations, bioconcentration factor, translocation factor, and hazard quotient of bamboo shoots. Significant differences in bacterial community structures were confirmed by principal coordinate analysis. Gemmatimonadetes, Actinobacteria, Chloroflexi, and Kaistobacter were identified as biomarkers that increased significantly in intercropping, enhancing the diversity of ecological functions in the rhizosphere. Redundancy analysis revealed that rhizosphere bacterial communities were significantly correlated with soil properties, especially TOC and available phosphorus. Intercropping could remarkably alter soil chemical and microbiological properties and facilitate ecosystem restoration by enhancing soil TOC sequestration, activating rhizobacterial community at the root‐soil interface, and finally increasing HMs removal. As the consumption of bamboo shoots grown in contaminated soils may pose health risks, more attention is needed on this issue in phytoremediation studies.