In the present research, the essential oil composition, bioactive compounds, anatomical and antioxidant activity of Achillea aucheri were investigated at four phenological stages. The yield of essential oil ranged from 0.1 % (five leaves appearance stage) to 0.7 % (full flowering stage). So, the oils from the plants harvested at the full flowering stage provided higher essential oil contents than those at other stages. The analysis of the essential oils by GC/MS revealed the presence of a large number of components represented mainly by oxygenated monoterpenes (24.36-77.81 %). The compounds revealed high variation at different phenological stages. The major constituents of A. aucheri were carvacrol (1.07-19.17 %), camphor (5.44-9.99 %), δ-cadinene (0.20-13.88 %), thymol (2.15-7.80 %), germacrene D (4.50-7.24 %), 1,8-cineole (1.62-5.54 %) and α-terpineol (1.71-3.42 %). The total phenolic (51.63 mg tannic acid/g DW) and flavonoid (10.88 mg quercetin/g W) contents were more accumulated at the 50 % flowering stage than others. The results revealed that the accumulation of essential oil in A. aucheri increased as the plant grew from the five leaves appearance stage to the 100 % flowering stage with increasing the size and number of secretory structures. Finally, the extracts collected at the 50 % flowering stage showed the highest antioxidant activity as measured based on FTC and DPPH method with the IC values ranging from 719.65 μg/mL to 1039.17 μg/mL for the samples.