Tree-herb intercropping is a prospective approach for the ecological remediation of soil contaminated with potentially toxic metals (PTMs). In this study, the facilitation and microbial community response of woody plant Morus alba L. intercropped with Cd/Zn hyperaccumulator Sedum alfredii H. and pioneer plant Arundo donax L. were carried out in the PTM-contaminated soil. The results indicated that the intercropping system can improve M. alba L. growth, as well as increase its PTMs uptake. The dried biomass of M. alba L. in the intercropping system was increased observably (p < 0.05) by 55.1%. Meanwhile, the contents of chlorophyll in M. alba L. leaves, PTMs contents in M. alba L. roots, and the relative abundance of Rhizobiaceae, Singulisphaera, Isosphaeraceae, and Arthrobacter in the M. alba L. rhizosphere were also notably (p < 0.05) enhanced. Meanwhile, the interactions of microorganisms in the intercropped plants rhizosphere might contribute to improving the biological quality of the contaminated soil. Soil sucrase and acid phosphatase activities in the intercropping system were significantly (p < 0.05) increased by 97.03% and 34.91% relative to the control. Furthermore, in the intercropping system, 93.61%, 61.30%, and 79.18% of Cd, Pb, and Zn were extracted by S. alfredii H., 72.16% of Cu was extracted by A. donax L., and 46.38% of Mn was extracted by M. alba L., which indicated that the extraction amounts of PTMs among the intercropped plants were relatively compensated. The results suggested that the tree-herb intercropping might increase the coexistence of plants and facilitate the adaptability for ecological remediation of PTM-contaminated soils.