Heat and cold stress influence the physiology and productivity of dairy cows. Milk metabolite profiling may provide valuable insights into breed-specific adaptive responses. Understanding these metabolic adaptations is crucial for improving breed resilience, productivity, and the nutritional quality of milk, particularly in the context of climate variability. This research investigates metabolic adaptations in cattle breeds under thermal stress conditions through milk metabolomic profiling using gas chromatography. The individual milk samples of 12 mid-lactating animals of Sahiwal, Tharparkar, and Karan Fries were collected from an organized dairy farm. Samples were collected in three different seasons viz: winter (December–January), thermo-neutral (March–April) and summer (May–June) seasons. The sample collection was done three times during each season (total number of samples in each season for each breed was n=36). In total, 158, 135, and 153 (in Sahiwal); 152, 138, and 153 (in Tharparkar); and 147, 105, and 131 (in Karan Fries) milk metabolites were identified during thermo-neutral, cold, and heat stress, respectively. During heat stress, Sahiwal cows demonstrated significant increase in acetic and butyric acids,with reductions in alanine and fumaric acid concentrations, indicating a metabolic shift toward anaerobic processes. Tharparkar showed increases in 9,12-octadecadienoic acid and threonine, which primarily impact the pentose phosphate pathway and unsaturated fatty acid biosynthesis. Karan Fries showed increase in dihydroxyacetone and valine but significant reductions in succinic acid, reflecting alterations in protein synthesis and energy metabolism. Under cold stress conditions, Sahiwal utilized branched-chain amino acid while Tharparkar cattle emphasized lipid metabolic pathways. Karan Fries cattle prioritized amino sugar metabolism for muscle maintenance. This study emphasizes breed-specific metabolic adaptations to thermal stress, providing insights into resilience mechanisms in indigenous breeds relative to crossbreds. Overall, these results emphasize the importance of breed-specific adaptations to thermal stress, which can inform management strategies aimed at enhancing productivity and welfare in dairy cattle.