Acknowledging the importance of medicinal compounds, flavonoids, and phenolic acids in plants and human health; understanding the best time to harvest the plant to get the most biological activity that can be therapeutic, and predicting and controlling the quality of medicinal plants are very useful. The rich chemical composition of medicinal wormwood (Artemisia absinthium L.), as well as its antioxidant activity, has led to its wide application in the pharmaceutical, cosmetic, and food industries. In the current research, phenological differences in phenolic content, the main constituents of essential oil, essential oil yield and antioxidant activity, and flavonoid content were evaluated. In this investigation, for all the factors, five replications were considered as completely randomized designs. The predominant natural components were alpha-pinene, alpha-phellandrene, cis-thujone, cis-chrysanthenol, epi-alpha-cadinol, beta-pinene, p-cymene, and trans-thujone. Some of the compounds such as alpha-pinene, alpha-phellandrene, cis-thujone and cis-chrysanthenol showed their highest amounts at vegetative stage. beta-Pinene, p-cymene, and trans-thujone had the highest amount at full flowering stage. The highest amount of total flavonoids, percentage of essential oil, sinapic acid and antioxidant activity were observed at vegetative growth. On the other hand, the highest trans-ferulic acid and chlorogenic acid content was observed at full flowering stage. Generally, this investigation provides beneficial evidence about the most appropriate harvest time for wormwood to produce the most favorable constituents for optimization in food, pharmaceutical, and herbal products.