Drought is a common abiotic stress that considerably limits crop production. The objective of this study is to explore the influence of water deficiency on the yield, physiologic and metabolomic attributes in upland cotton cultivars (Gossypium hirsutum L). Cotton cultivars, 'Ishonch' and 'Tashkent-6' were selected to study the relationships among their physiologic, metabolomic and yield attributes during water deficiency. Deficit irrigation was designed by modifying the traditional watering protocol to reduce water use. Results indicate that cotton cultivars respond differently to water deficit stress. Water deficit significantly influenced plant height, the number of internodes, and sympodial branches in both cultivars. However, yield components such as the number of bolls, boll seed, lint mass, and individual plant yield were significantly reduced only in 'Tashkent-6'. The leaf area decreased and the specific leaf weight increased in 'Ishonch' under deficit irrigation conditions. However, 'Tashkent-6' demonstrated significant water loss compared to 'Ishonch', and both cultivars showed reduced transpiration rates. Untargeted metabolite profiles of leaves showed clear separation in 'Ishonch', but not in 'Tashkent-6' under deficit irrigation compared to full irrigation. The individual metabolites such as proline and galactinol showed strong association with yield under water deficit stress. Moreover, this study indicates that leaf area and transpiration intensity influence yield during water deficiency. In summary, the correlation among morpho-physiologic, metabolic, and yield components significantly varied between the two cultivars under water deficiency. The flowering stage was sensitive to water stress for both cultivars. The direct relationship between physiology, metabolism, and yield may be a useful selection criterion for determining candidate parents for cotton drought tolerance breeding.