In order to determine the response of seed germination and seedling root system of island cotton to salt stress, and to screen out island cotton varieties with high salt tolerance, an experiment was conducted using main sea island cotton varieties Xinhai 31, Xinhai 35, Xinhai 43, and Xinhai 48 grown in Xinxiang Aksu area, with treatment of neutral salt (neutral salt) mixed with NaCl, Na2SO4 at 1:1 of mole ratio and treatment of alkali salt (alkaline salt) mixed with NaCl and NaHCO3 at 1:1 of mole ratio, Total salt concentration (Na +) was 0, 120, 180, 240, 300, and 360 mmol L -1. Seed germination and seedling root growth parameters of island cotton under the stress were measured. The germination parameters, biomass, root and crown ratio, salt sensitivity index, salt tolerance index, root length, root surface area and root volume of the island cotton seeds decreased with the increase of salt concentration. Moreover, under high salt concentration, there was a significant negative correlation of plant height, root biomass, stem and leaf biomass with salt concentration, indicating that high salt environment inhibited cotton seed germination and normal growth of seedlings. Under the concentration of 120 mmol L -1, the total length of the root system of Xinhai 48 treated with neutral salt did not increase significantly compared with that of the control group, while that of the other varieties increased significantly. There was no significant difference in the total volume and total surface area of the roots. The low salt concentration promoted the elongation and growth of the fine roots (d ≤ 0.5 mm). The middle root (0.5 < d ≤ 2.0 mm) of Xinhai 43 increased significantly than that of CK, resulting in a significant increase in total root volume and total surface area. The total length, surface area, and volume in alkaline salt treatment were not significantly different from those of Xinhai 31 and the control, while decreased significantly in other varieties. At the concentration of 180-240 mmol L -1, the total length, surface area and volume of roots in neutral salt treatment had a significant decrease compared with these of the control except for Xinhai 43; there was no significant difference among all varieties; lot a decrease in alkaline salt treatment. Among them, the total length of the roots of Xinhai 35 decreased more slowly than that of other varieties. At the concentration of 300-360 mmol L -1, the total root length, volume and surface area of the two salt varieties dropped sharply. The alkaline salt stress had a more significant decrease effect than the neutral salt stress. Under the conditions of this experiment, the normal growth of island cotton seedlings could withstand the salt concentration of 240 mmol L -1, but the damage of alkaline salt to island cotton seedlings was much greater than that of neutral salt. The order of salt tolerance of the tested varieties was Xinhai 35, Xinhai 43, Xinhai 31, and Xinhai 48.