To determine the genotypic variation in response to salt (NaCl) stress in cotton (Gossypium hirsutum L.) seedlings, potassium (K +) and sodium (Na +) homeostasis, photochemical energy utility, reactive oxygen metabolism and the activity of antioxidant enzymes were comparatively analyzed in three cotton cultivars (CCRI 49, CCRI 35 and Z 51504) under salt constraint. The results showed that NaCl treatment significantly inhibited biomass accumulation, and the extent of inhibition was highest in CCRI 49 and lowest in Z 51504. Salinity caused an ion imbalance in plants but ion homeostasis was less pronounced in Z 51504, as it accumulated more K + and less Na +. Experiments of salt shock treatment were tested using a non-invasive micro-test (NMT) system, which also revealed that Z 51504 had lower Na + influx and better K + retention. Salinity increased excess-energy dissipation [non-photochemical quenching (qN) and photorespiration rate (PR)], but depressed photochemical efficiency such as photosynthesis rate (P n), quenching (qP), photochemical quantum yield of photosystem (Φ PSII) and electron transport rate (ETR). As a result, more electrons were driven to other sinks, for example decreasing ETR/P n and increasing the O 2 − generation rate. However, the superior tolerance of Z 51504 had a better balance of photochemical energy under salt conditions, displayed higher photochemical efficiency and excess-energy dissipation. Furthermore, the antioxidant enzyme activities were also affected by salt stress and less effectively removed reactive oxygen species. The antioxidant enzyme activities of Z 51504 were higher than those of CCRI 49 and CCRI 35, which resulted in lower levels of reactive oxygen species (ROS) and mitigated the salt-induced membrane lipid peroxidation. The overall results indicated that more effective retention of ions, photochemical energy utility and ROSremoving capability were probably the main reasons for the stronger salt tolerance in Z 51504.