The effect of different NaCl concentrations (control, 2, 4 and 6 dS/m) and three harvesting times in different seasons including spring (9 April), summer (5 July), and fall (23 September) was evaluated on essential oil (EO) yield, composition, phenolic, flavonoid content, and antioxidant activity of myrtle. Essential oil yield ranged from 0.2% in control and fall to 1.6% in moderate salinity (4 dS/m) and spring season. The main constituents obtained from gas chromatography/mass spectrometry analysis were α-pinene, 1,8-cineole, limonene, linalool, α-terpineol, and linalyl acetate in which α-pinene ranged from 11.70% in moderate and fall to 30.99% in low salinity (2 dS/m) and spring, while 1,8-cineole varied from 7.42% in high salinity (6 dS/m) and summer to 15.45% in low salinity and spring, respectively. Salt stress also resulted in an increase in total phenolic, flavonoid content, and antioxidant activity. The highest antioxidant activity based on DPPH radical scavenging activity, reducing power (FTC) and β-carotene/linoleic acid model systems was found in plants harvested in spring and summer in high stress condition. The lowest IC values obtained in 6 dS/m in spring (375.23 μg/ml) followed by summer (249.41 μg/ml) and fall (618.38 μg/ml). Eight major phenolic and flavonoid compounds were determined in three harvesting times using high performance liquid chromatography analysis. In overall, late harvesting time of myrtle in fall can lead to reduce the most of major EO components, while it can improve the amount of phenolic acids.