High temperature during reproductive stages of cotton is a major constraint to achieve potential yield of cotton. The aim of the present study was to determine comparative thermo-sensitivity of squaring and flowering, to optimize exogenous selenium for heat-stressed cotton, and to explore correlation among physiochemical and morphological attributes. The experiment was conducted during 2013 and repeated during 2014. The experiment was laid out in randomized complete block design under split plot arrangement and replicated thrice. Treatments were comprised of heat stress (H 0 = no heat imposition; H 1 = heat imposition at squaring; and H 2 = heat imposition at flowering) in main plot and varying foliar selenium concentrations (Se 0 = water spray/control; Se 50 = 50; Se 100 = 100; and Se 150 = 150 mg L-1 selenium) in split plot. Significantly, more antioxidants, chlorophyll contents, water relation attributes, seed cotton yield, and lesser hydrogen peroxide were recorded with 150 mg L-1 foliar selenium compared with other concentrations under H 0. While under H 1 and H 2 , statistically similar and significantly more antioxidants, chlorophyll contents, water relation attributes, seed cotton yield, and lesser hydrogen peroxide were observed for 100 and 150 mg L-1 selenium compared with other selenium concentrations. Conclusively, H 2 proved more thermolabile compared with H 1 , and application of 150 mg L-1 foliar selenium effectively alleviated adverse effects of heat. Moreover, we observed strong and significant associations of all physiochemical attributes with seed cotton yield.