Soil microorganisms, which intricately link to ecosystem functions, are pivotal for the ecological restoration of heavy metal-contaminated soil. Despite the importance of rare and abundant microbial taxa in maintaining soil ecological function, the taxonomic and functional changes in rare and abundant communities during in situ chemical stabilization of cadmium (Cd)-contaminated soil and their contributions to the restoration of ecosystem functions remain elusive. Here, a 3-year field experiment was conducted to assess the effects of five soil amendments (CaCO3 as well as biochar and rice straw, individually or in combination with CaCO3) on rare and abundant microbial communities. The rare bacterial community exhibited a narrower niche breadth to soil pH and Cd speciation than the abundant community and was more sensitive to environmental changes altered by different soil amendments. However, soil amendments had comparable impacts on rare and abundant fungal communities. The assemblies of rare and abundant bacterial communities were dominated by variable selection and stochastic processes (dispersal limitation and undominated processes), respectively, while assemblies of both rare and abundant fungal communities were governed by dispersal limitation. Changes in soil pH, Cd speciation, and soil organic matter (SOM) by soil amendments may play essential roles in community assembly of rare bacterial taxa. Furthermore, the restored ecosystem multifunctionality by different amendments was closely related to the recovery of specific keystone species, especially rare bacterial taxa (Gemmatimonadaceae and Haliangiaceae) and rare fungal taxa (Ascomycota). Together, our results highlight the distinct responses of rare and abundant microbial taxa to soil amendments and their linkage with ecosystem multifunctionality. IMPORTANCE Understanding the ecological roles of rare and abundant species in the restoration of soil ecosystem functions is crucial to remediation of heavy metal-polluted soil. Our study assessed the efficiencies of five commonly used soil amendments on recovery of ecosystem multifunctionality and emphasized the relative contributions of rare and abundant microbial communities to ecosystem multifunctionality. We found great discrepancies in community composition, assembly, niche breadth, and environmental responses between rare and abundant communities during in situ chemical stabilization of Cd-contaminated soil. Application of different soil amendments triggered recovery of specific key microbial species, which were highly related to ecosystem multifunctionality. Together, our results highlighted the importance of rare bacterial as well as rare and abundant fungal communities underpinning restoration of soil ecosystem multifunctionality during the Cd stabilization process.