Thymus Kotschyanus, as a native plant of Iran, is considered to be one of the most important medicinal plants with its unique properties. To evaluation of the effect of salinity and humic acid (HA) on aerial yield essential oil content, a factorial experiment was conducted based on a Completely Randomized Design (CRD) with five replications in 2014 in Qom, Iran. The first factor was five native accessions of T. kotschyanus, the second factor was salinity stress like control (0), 50, 100, 150 and 200 mM sodium chloride and the third factor was humic acid with three levels of 0, 1.5 and 3.0 g/l. Data were collected for seedling growth characteristics and essential oil content. The results of the analysis of variance showed significant effects of genotype, salinity on all of the traits. The effect of HA was significant on stem length, root length, aerial dry weight, and dry root weight. There were significant interaction effects for salinity by humic acid (root length, root weight, and essential oil content), for salinity by genotypes (stem length, root/shoot length ratio, essential oil yield) and for HA by genotype (root dry weight and essential oil yield). Results of means comparison between accessions showed that accession Divandarre had higher mean values for all of the traits except stem length and oil content. Results showed that by increasing salinity stress, all of the traits except root dry weight and RS were decreased. The application of HA was effective only on stem and root length. It was concluded that low salinity (50 mM NaCl) coupled 1.5 g/l HA had increased both essential oil content and oil production in all of the accessions. The response of Divandarre to salinity through the application of HA was positively higher than other accessions.