To investigate the effects of Zinc-salicylic acid nano-complex and storage time on horticultural and phytochemical properties of Thymus daenensis Celak, a factorial experiment was conducted based on a randomized complete block design. Foliar spraying was done in two stages 15 days after establishment, at levels of zero, 0.1, 0.3 and 0.5% by volume. After harvesting and storage during periods of 0, 2, 4 and 6 months at room temperature, quantitative and qualitative changes in essential oil, phenolic compounds content and antioxidant activity of shoots were studied. Based on the foliar application of zinc-salicylic acid nanocomplex by 0.3%, it increased plant height, fresh weight, dry weight, flower height, leaf length, leaf width and wet to dry weight ratio, respectively, compared to the control without foliar application by 32.5, 26.7, 19.2, 38.3, 22.2 and 27.08%, respectively. Storage time had no significant effect on the percentage of essential oil. Concentration of 0.3% nanocomplex increased the essential oil by 0.822% compared to the control. The effect of interaction between nanocomplex concentration and storage time on the percentage of essential oil was not significant. The predominant compounds were essential oil, Carvacrol, Thymol, p-Cymene and Borneol. The highest antioxidant activity of plant extract was related to the interaction of foliar application of zinc-salicylic acid nanocomplex with a concentration of 0.1% and storage for 60 days. Treatment with zinc-salicylic acid nanocomplex (at a concentration of 0.3%) improved vegetative characteristics and storage time and increased the percentage of essential oil.