Tree-herb co-planting is regarded as an ecologically sustainable approach for the remediation of metal(loid)-contaminated soil. In this study, two herb species, Pteris vittata L. and Arundo donax L., and two woody species, Morus alba L. and Broussonetia papyrifera L., were selected for the tree-herb co-planting, and their impacts on the changing of microbial community structure in metal(loid)-contaminated soil were studied by high-throughput sequencing. The results showed that the microbial diversity was stably maintained by the tree-herb interactions, while the composition of the microbial community was clearly affected in metal(loid)-contaminated soil. According to the Venn and flower diagrams, heat map and principal coordinate analysis, both plant monocultures and co-planting had specific microbial community structures, which suggested that the composition and abundance of bacterial communities varied between plant monoculture and tree-herb co-planting treatments. In particular, A. donax L. played a vital role in increasing the abundances of Cyanobacteria (>1%) in metal(loid)-contaminated soil when co-planted with woody plants. Furthermore, some specific microorganisms combined with plants played a key role in improving enzyme activity in the contaminated soil. Correspondingly, sucrase and acid phosphatase activities in monoculture and co-planting treatments significantly (p < 0.05) increased by 1.05-3.37 and 7.24-20.3 times. These results indicated that the rhizospheric interactions in the tree-herb co-planting system positively affected the soil microbes and had stronger impacts on the composition of soil microorganisms, which was closely related to the improvement of the biological quality in the metal(loid)-contaminated soil.