Drought stress is one of the major environmental constraints on the productivity and quality of aromatic and medicinal plants. The purpose of this study was to compare the morphological, physiological, biochemical, and phenolic responses of three Thymus species (T. serpyllum, T. vulgaris, and T. kotschyanus) to different irrigation regimes: 100%, 70%, and 40% of field capacity. The results revealed species-specific differences in drought tolerance. T. kotschyanus exhibited the highest drought resistance, maintaining greater relative water content and biomass under stress, while T. serpyllum showed the most significant decreases. Proline accumulation increased linearly with drought severity in all species, indicating osmotic adjustment under drought stress. T. vulgaris had lower chlorophyll and carotenoid contents, whereas T. kotschyanus had higher levels under severe drought. Total phenolic and flavonoid contents increased significantly in all species. T. kotschyanus had the highest essential oil percentage under severe drought, indicating the potential for drought-adapted essential oil production. HPLC profiling identified rosmarinic acid as the dominant phenolic compound, particularly in T. kotschyanus, where its content increased by 47% under stress. Overall, the findings show that Thymus species have distinct adaptive mechanisms, with T. kotschyanus exhibiting superior drought tolerance and phytochemical resilience, making it a promising candidate for cultivation in arid and semi-arid regions.