Salt stress negatively affects crop survival, growth, development, and yield. Methyl salicylate (MeSA) is synthesized from salicylic acid (SA) which is a volatile organic compound that is responsible for inducing defense mechanisms in plants and also has a protective role in stress sensitivity. The objective of this study was to examine the effect of different concentrations of methyl salicylate (MeSA) on the physiological and biochemical characteristics of two rice varieties GRIS4 (G1) and GRIS5 (G2) under salt stress at the seedling stage. Five hundred seeds of each variety were treated with different doses of MeSA (0, 0.1, 0.5, and 1.0 mM) and screening various salinity levels (0, 6, 8, 12, 15, and 17 dS m-1) at the seedling stage (21 days old). The different traits such as survival rates, morphological characteristics including plant height and root and length, the biomass of fresh and dry weights of the shoots and roots, and biochemical parameters (chlorophyll a and b, proline, and phenolic and flavonoid content) were measured. Treatment 0.1 mM MeSA had significantly higher root length and dry weight under 8 dS m-1, 6 dS m-1, higher chlorophyll and phenolic content under 17 dS m-1 for G1, whereas the 0.1 mM MeSA-treated plants had significantly higher root length under 15 dS m-1 and root fresh weight under 12 dS m-1 for G2 compared to control plants. The 0.5 mM MeSA-treated plants had significantly higher seedling length, survival rate, root fresh weight, and shoot fresh weight under 8 dS m-1, 6 dS m-1 then also had higher proline and flavonoid content under 17 dS m-1 for G1, while G2 had higher shoot dry weight under 17 dS m-1, higher root fresh weight under 8 dS m-1, higher proline content under15 dS m-1, and higher phenolic and flavonoid contents under 12 dS m-1 compared to control plants. Treatment 1.0 mM MeSA had higher survival rate under 6 dS m-1, seedling length under 15 dS m-1, shoot fresh weight under 6 dS m-1, root dry weight under 8 dS m-1, chlorophyll a under 15 dS m-1, and chlorophyll b under 8 dS m-1 compared to control plants. These results showed that positive effects induced by MeSA increased some physiological and biochemical traits of rice under salt stress at the seedling stage.