Adopting a potting method with two Sea Island cotton varieties, Xinhai 21 and Xinhai 34, and two Upland cotton varieties, Xinluzao 50 and Xinluzao 57, as materials, we examined changes in growth, chlorophyll content, net photosynthetic rate, transpiration rate, antioxidant enzyme activity, osmotic adjustment substances and malondialdehyde (MDA) content between Sea Island cotton and Upland cotton under NaCl stress. With increasing salt concentration in soil, the growth, chlorophyll content, net photosynthetic rate and transpiration rate indicators declined to different degrees in the four varieties, whereas peroxidase (POD), superoxide dismutase (SOD) and soluble sugar content showed a trend of increasing first in level and then decreasing with increasing salt concentration, proline and malondialdehyde content. Xinhai 21 and 34 showed less impact of stress than Xinluzao 57 and 50. Under 0.6% NaCl, the Sea Island cotton and Upland cotton cultivars showed good salt tolerance. The difference in salt tolerance between the two cultivated species was not significant. However, the growth of the four varieties was inhibited under 0.8% and 1.0% NaCl stress. Xinluzao 57 and 50 seedlings grew slowly, with small leaf area and little dry matter accumulation and even death. Leaves of cotton seedlings were sensitive to salt stress; the growth of leaf width and leaf length was inhibited with increasing salt concentration, which could be used as an index to select salt-tolerant varieties.