Thyme is widely distributed in the worldwild. In China, there are 15 species, 2 varieties and 1 variant. Thymus quinquecostatus which contains abundant bioactive terpenoids is an important wild medicinal and aromatic plant in Chinese native thymes. Thymus vulgaris ‘Elsbeth’ comes from Europe and is known for its medicinal properties. The terpenoids exist in the glandular trichomes (GTs), a special epidemal structure. In Lamiaceae, glandular trichomes usually include peltate glandular trichomes (PGTs) and capitate glandular trichomes (CGTs). In previous study, we had analysed the molecular mechanisms of GTs but the formation process was not revealed. In this study, we observed the formation of PGTs and CGTs in thyme. The PGT underwent the complex process, including the basal, stalk, and head cells, there were 8-12 head cells. The CGT also had three cells, but its head cell only had one cell. Meanwhile, molecular biology research was carried out and we identified 68 HD-ZIP proteins and selected several key genes related to the formation of GTs according to the expression levels. Then, we cloned an HD-ZIP Ⅳ transcription factor TqHD1 from T. quinquecostatus and characterized it. TqHD1 not only can promote the formation of GTs but also can lead to the changes of volatile components and some relative genes levels. These findings complete the study of cell micromorphology of thyme and lay the foundation for characterization of factors in epidermis-related functions in thyme.