Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.