Trichomes are attractive cells for terpenoid biosynthesis and accumulation inArtemisia annua. However, the molecular process underlying the trichome ofA. annuais not yet fully elucidated. In this study, an analysis of multi-tissue transcriptome data was performed to examine trichome-specific expression patterns. A total of 6646 genes were screened and highly expressed in trichomes, including artemisinin biosynthetic genes such asamorpha-4,11-diene synthase(ADS) andcytochrome P450 monooxygenase(CYP71AV1). Mapman and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that trichome-specific genes were mainly enriched in lipid metabolism and terpenoid metabolism. These trichome-specific genes were analyzed by a weighted gene co-expression network analysis (WGCNA), and the blue module linked to terpenoid backbone biosynthesis was determined. Hub genes correlated with the artemisinin biosynthetic genes were selected based on TOM value.ORA,Benzoate carboxyl methyltransferase(BAMT),Lysine histidine transporter-like 8(AATL1),Ubiquitin-like protease 1(Ulp1) andTUBBYwere revealed as key hub genes induced by methyl jasmonate (MeJA) for regulating artemisinin biosynthesis. In summary, the identified trichome-specific genes, modules, pathways and hub genes provide clues and shed light on the potential regulatory mechanisms of artemisinin biosynthesis in trichomes inA. annua.