Soil salinity is one of the major abiotic stresses having adverse effects on crop productivity and quality. Cotton is the most important cash crop in Xinjiang. Extensive research has been conducted on the effects of salinity on cotton and cotton plant is classified as moderately salt-resistant species in terrestrial plant in most of documents. However, almost all of these researches were focused on upland cotton. Sea island cotton is another cultivation species of cotton, which was distributed only in xinjiang in China and is widely cultivated due to it adopted to weather in Xinjiang and its relatively higher economical values. Few studies documented on effects of salinity stress on the growth and development of sea island cotton as well as its internal adaptive mechanisms. Therefore, this paper try to ascertain mechanism of the eco-physiological sea island cotton adapting to salt stress, supply theoretical foundations and reference index for cultivate management, resistant screening, breeding of sea island cotton. Two cotton cultivars with varied salt-tolerance ability was selected to study sea cotton's response when exposed to salt environment. Xinhai 28(XH 28) is a salt-resistance sea island cotton cultivar while Xinhai 21(XH 21) is a salt-sensitive sea island cotton cultivar. The experiment was conducted in a growth chamber, water culture experiments were carried out to study the effects of salinity stress on seed germination and seedling growth. Full nutritional solution was used in at germination stages, NaCl was added to solution at 3 full expand leaves stages at 6 NaCl levels(0, 50, 100, 150, 200 and 250 mmol?L-1). All nutrient solutions were changed once per 3 days and deionized water was added daily to replace the water lost by transpiration. The seedlings were salt-stressed for 30 days, then was sampled and tested for biomass partitioning, soluble protein, Proline (Pro) contents, as well as activities of peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) activities in leaves and roots of the XH 28 and XH 21. The results showed that (1)Fresh weight of sea island cotton was more sensitive to salt stress as compared to dry weight，shoots were more sensitive as compared to roots; (2) Higher proline content was observed both in the roots and leaves when cotton seedling was stressed by salt; (3) Root length, plant height and fresh-dry weight of XH 28 were significantly increased under low NaCl concentration (≤50 mmol?L-1) stress; (4) Salt stress resulted in the decrease of soluble protein in roots of sea island cotton, while soluble protein was enhanced in leaves; (5) Activities of POD, CAT and APX in roots and leaves in NaCl tolerant genotype were significantly higher than that in NaCl sensitive genotype. Whereas activity of GR in roots and leaves was lower in XH 21. In conclusion, low concentration of NaCl can stimulate plant growth and, consequently, result in higher biomass. Protein and proline content increase in roots and leaves and the higher active of activities of POD, CAT and APX can be considered as the physiological characteristics in NaCl tolerant genotypes of sea island cotton.