The aim of the current study was to demonstrate the presence of different secretory structures of thyme essential oil on the leaf surfaces identified by SEM apparatus, and the phytonutrients content of aqueous extracts of aerial parts of Tunisian Thymus hirtus Willd. Ssp. algeriensis Boiss. and Reut. and also to compare the difference in terpenic compounds at three developmental stages. The phenolic and terpenic compounds found in thyme aerial parts were determined by HPLC and GC/MS apparatus, respectively. Two kinds of glandular trichome (peltate and capitate) are the main site of production and secretion of essential oils. Two types of capitate hairs were observed, the first one was with short stalk, neck and cellular secretory head, and the second one was with long stalk composed of one to many cells. Non glandular trichomes are densely distributed in the Thymus hirtus Willd. Ssp. algeriensis Boiss. and Reut. species. The results obtained by chromatographic analysis revealed the richness of thyme, harvested during vegetative phase, in bioactive phytochemicals, that include gallic acid, coumaric acid, catechin, rutin and quercetin compared to other samples. Terpenic and phenolic compounds levels increased over stages. A total of 65 terpenic constituents and others identified by GC/MS and representing 93.01 to 99.59% of the total essential oil. Antioxidant and antibacterial activities varies throughout growing season in aerial parts of Thymus hirtus Willd. Ssp. algeriensis Boiss. and Reut. At vegetative stage, the essential oils showed the highest antioxidant potential and inhibition zone (IZ) on differents bacterial strains, to the high effect as chloramphenicol and Fosfomycin.