Exploring the genetic network of glandular trichomes and manipulating genes relevant to secondary metabolite biosynthesis are of great importance and value. Artemisinin, a key antimalarial drug ingredient, is synthesized and stored in glandular secretory trichomes (GSTs) in Artemisia annua. WIN/SHN proteins, a clade of AP2/ERF family, are known as regulators for cuticle biosynthesis. However, their function in glandular trichome development is less unknown. In this study, we identified a WIN/SHN gene from A. annua and named it as AaWIN1. AaWIN1 was predominantly expressed in buds, flowers and trichomes, and encoded a nuclear-localized protein. Overexpressing AaWIN1 in A. annua significantly increased the density of GST as well as the artemisinin content. Furthermore, AaGSW2 was reported to play an important role in promoting GST initiation, and the expression of AaGSW2 was induced in AaWIN1-overexpression lines. AaMIXTA1, a MYB protein positively regulating trichome initiation and cuticle biosynthesis, was confirmed to interact with AaWIN1. In addition, the ectopic expression of AaWIN1 resulted in slender and curled leaves, fewer trichomes, and rising expressions of cuticle biosynthesis genes in Arabidopsis thaliana. Taken together, based on phenotype observations, content measurements and gene expression detections, AaWIN1 was considered as a positive regulator for GST initiation in A. annua.