The production of cotton is negatively affected by salinity. For this purpose, 8 parents and their 16 F1 hybrids were evaluated under saline stress (15 dSm(-1)) in Line x Tester fashion. Mean values of plant height, number of bolls plant(-1), boll weight, lint weight, seed cotton yield plant(-1), seed index, no. of seeds boll(-1), seed mass boll(-1), lint mass boll(-1), seed volume per 100 seeds, fiber strength, fiber length, lint%, K+, K+/Na+ ratio, CAT, TSP, chlorophyll a, b, and relative water contents decreased under salt stress whilst the values of lint index, seed density, fiber fineness, Na+, H2O2, SOD, POD carotenoids, malondialdehyde, phenolic contents, ascorbic acid, and flavonoids increased under saline conditions. Under saline MS-71x CRS-2007, MS-71x KAHKASHAN, and IUB-65 x FH-312 exhibited performed better than other genotypes for most traits. For fiber quality traits IUB-65x CRS-2007 and IUB-65x FH-312 showed the highest value under salt stress. Improved identified cotton genotypes can enhance our capacity to grow cotton in salt-affected soils and the key morpho-biochemical traits can potentially be exploited to obtain higher and more stable crops yield under stressed environments.