Heat and drought stresses are presently the principal risk on world's food quantity, limiting yield. Both of these two stresses affect plants metabolism, physiological and morphological processes, which ultimately reduces the productivity. The plant cell develops different stress induced self-defence mechanisms to reduce the effect of stresses. These defence mechanisms are developed by modifying gene expression pattern, which results in qualitative and quantitative deviations in proteins synthesis, leading to the modulation of certain metabolic and defensive pathways. New metabolic profiling technologies offer a great opportunity for biologist to understand defence mechanism of plants under stress conditions. Metabolomics technologies presently enabled the using of different multi-variate analyses, generated from various hyphenated and chromatographic discovery systems, such as gas or liquid chromatography together with mass spectrometry, or nuclear magnetic resonance (NMR) based methods. Investigation and mining of metabolomics data can be done through a blend of different statistical methods, such as independent component analysis and analysis of variance. Metabolomics in combination with gene expression, protein interaction and other different regulatory pathways can be useful to diverse organisms with trivial alterations. In recent time, this technology has been used to investigate drought tolerance in plant crops to find particular stress related patterns in metabolic expression. These studies identified the vital roles of primary and secondary metabolites associated with abiotic stress tolerance.