Glandular secretory trichomes (GSTs) are regarded as biofactories for synthesizing, storing, and secreting artemisinin. It is necessary to figure out the initiation and development regulatory mechanism of GSTs to cultivate high-yielding Artemisia annua. Here, we identified an MYB transcription factor, AaTAR2, from bioinformatics analysis of the A.annua genome database and Arabidopsis trichome development-related genes. AaTAR2 is mainly expressed in young leaves and located in the nucleus. Repression and overexpression of AaTAR2 resulted in a decrease and increase, respectively, in the GSTs numbers, leaf biomass, and the artemisinin content in transgenic plants. Furthermore, the morphological characteristics changed obviously in trichomes, suggesting AaTAR2 plays a key role in trichome formation. In addition, the expression of flavonoid biosynthesis genes and total flavonoid content increased dramatically in AaTAR2-overexpressing transgenic plants. Owing to flavonoids possibly counteracting emerging resistance to artemisinin in Plasmodium species, AaTAR2 is a potential target to improve the effect of artemisinin in clinical therapy. Taken together, AaTAR2 positively regulates trichome development and artemisinin and flavonoid biosynthesis. A better understanding of this 'multiple functions' transcription factor may enable enhanced artemisinin and flavonoids yield. AaTAR2 is a potential breeding target for cultivating high-quality A.annua.