Drought stress is a major abiotic factor affecting the growth and productivity of brinjal (Solanum melongena L.). In this study, we evaluated the effect of drought stress on morphological, physiological and metabolomic response in susceptible genotypes Solanum melongena var. insanum, CO-2 and tolerant genotype Arka Harshitha at three timepoints.The results showed that drought stress significantly reduced the shoot length, root length, biomass, leaf area, photosynthetic rate and intrinsic water use efficiency in susceptible genotypes, while the tolerant genotype Arka Harshitha maintained comparatively higher growth rates, leaf area, photosynthetic rate and water use efficiency. Further, Arka Harshitha exhibited lower lipid peroxidation and higher antioxidant enzyme activity at all the time interval compared to the susceptible genotypes. Additionally, genotype specific sugar accumulation patterns were observed in root and leaf sugars under control and drought conditions. In the presence of drought stress, the tolerant genotype Arka Harshitha exhibited elevated concentrations of glucose, fructose, sucrose, mannose, inositol, and fucose. Conversely, the susceptible genotype Solanum melongena var. insanum accumulated xylose, arabinose, mannose, fructose, glucose, and sucrose sugars. Higher content of these sugars may positively regulate energy metabolism, osmotic adjustment, and signaling under drought conferring response to drought stress. The results from principal component analysis indicate that fructose, glucose, ribose, xylose, sucrose, sorbitol, arabinose, mannose, ribose, and fucose are expected to play a positive and significant role in the drought tolerance of brinjal. These findings provide an initial insight on importance of differential responses in sugar accumulation under drought stress.