A study was conducted on the effect of nano-complex salicylic acid-zinc on the physiological and biochemical characteristics of Thymus Daenensis Celak. The treatments were applied in two stages, 15 days apart, after the establishment, in May as spraying at zero, 0.1, 0.3, and 0.5% (v/v). Based on the results, different levels of nano-complex salicylic acid-zinc led to a change in the vegetative growth indices studied, percentage of essential oil compounds, polyphenolic content, and antioxidant activity. The most important compounds in the essential oil were reported in the control treatment: Carvacrol, Thymol, p-cymene, Borneol, and 1.8-cineole. A 0.5% solution of nano-complex salicylic acid-zinc increased the amount of Carvacrol in essential oil by 80.7% compared to the control. The amount and type of polyphenolic compounds were measured with HPLC. The most important compounds included rosmarinic acid, Thymol, Carvacrol, and Hesperetin. The best treatment for increasing polyphenols was concentration of 0.5% of nano-complex salicylic acid-zinc.