Red flour beetle (Tribolium castaneum) is one of the most destructive pests of stored cereals worldwide. The essential oil (EO) ofArtemisia vulgaris(mugwort) is known to be a strong toxicant that inhibits the growth, development, and reproduction ofT. castaneum. However, the molecular mechanisms underlying the toxic effects ofA. vulgarisEO onT. castaneumremain unclear. Here, two detoxifying enzymes, carboxylesterase (CarEs) and cytochrome oxidase P450 (CYPs), were dramatically increased in red flour beetle larvae when they were exposed toA. vulgarisEO. Further, 758 genes were differentially expressed between EO treated and control samples. Based on Gene Ontology (GO) analysis, numerous differentially expressed genes (DEGs) were enriched for terms related to the regulation of biological processes, response to stimulus, and antigen processing and presentation. Our results indicated thatA. vulgarisEO disturbed the antioxidant activity in larvae and partially inhibited serine protease (SP), cathepsin (CAT), and lipase signaling pathways, thus disrupting larval development and reproduction as well as down-regulating the stress response. Moreover, these DEGs showed thatA. vulgarisindirectly affected the development and reproduction of beetles by inducing the expression of genes encoding copper-zinc-superoxide dismutase (CuZnSOD), heme peroxidase (HPX), antioxidant enzymes, and transcription factors. Moreover, the majority of DEGs were mapped to the drug metabolism pathway in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Notably, the following genes were detected: 6odorant binding proteins(OBPs), 5chemosensory proteins(CSPs), 14CYPs, 3esterases(ESTs), 5glutathione S-transferases(GSTs), 6UDP-glucuronosyltransferases(UGTs), and 2multidrug resistance proteins(MRPs), of which 8CYPs, 2ESTs, 2GSTs, and 3UGTswere up-regulated dramatically after exposure toA. vulgarisEO. The residual DEGs were significantly down-regulated in EO exposed larvae, implying that partial compensation of metabolism detoxification existed in treated beetles. Furthermore,A. vulgarisEO induced overexpression ofOBP/CYP, and RNAi against these genes significantly increased mortality of larvae exposed to EO, providing further evidence for the involvement ofOBP/CYPin EO metabolic detoxification inT. castaneum. Our results provide an overview of the transcriptomic changes inT. castaneumin response toA. vulgarisEO.