Thyme as a perennial herb has been recognized globally for its antimicrobial, antiseptic and spasmolytic effects. In this investigation, we have used non-targeted metabolite and volatile profiling combined with the morpho-physiological parameters in order to understand the responses at the metabolite and physiological level in drought sensitive and tolerant thyme plant populations. The results at the metabolic level identified the significantly affected metabolites. Significant metabolites belonging to different chemical classes consisting amino acids, carbohydrates, organic acids and lipids have been compared in tolerant and sensitive plants. These compounds may take a role through mechanisms including osmotic adjustment, ROS scavenging, cellular components protection and membrane lipid changes, hormone inductions in which the key metabolites were proline, betain, mannitol, sorbitol, ascorbate, jasmonate, unsaturated fatty acids and tocopherol. Regarding with volatile profiling, sensitive plants showed an increased-then-decreased trend at major terpenes apart from alpha-cubebene and germacrene-D. In contrast, tolerant populations had unchanged terpenes during the water stress period with an elevation at last day. These results suggesting that the two populations are employing different strategies. The combination of metabolite profiling and physiological parameters assisted to understand precisely the mechanisms of plant response at volatile metabolome level.