Abstract: 【Objective】 To study the response mechanism of cotton seedlings in response to salt stress, and to provide experimental basis for the screening of salt-tolerant varieties of cotton. 【Methods】 Salt-tolerant and sensitive cotton seedlings were treated with 200 mM NaCl at the three-leaf stage, and the microstructures of cotton leaves were observed, and physiological and biochemical indexes were analyzed at 0, 48 h and 48 h of re-watering under NaCl treatment. 【Results】 Salt-tolerant and sensitive seedlings gradually softened their leaves and stalks under NaCl stress from 0-48 h. Sensitive seedlings withered and faded their cotyledons and slightly scorched the margins of the true leaves under NaCl treatment. The malondialdehyde concentration of cotton leaves was significantly elevated, and the chlorophyll content and the activity of superoxide dismutase were significantly reduced under NaCl treatment. After re-watering, both salt-tolerant and sensitive types were somewhat restored, malondialdehyde concentration was reduced, and chlorophyll content, superoxide dismutase activity and peroxidase activity were increased.Under salt stress conditions, leaf thickness, fenestrated tissue thickness and spongy tissue thickness of salt-tolerant and sensitive types decreased, and the SS type of sensitive material decreased more, and the difference was significant compared with normal conditions, but both materials recovered after re-watering, and the salt-tolerant material recovered better. 【Conclusion】 NaCl treatment for 48 h not only has an effect on the physiological and biochemical levels of cotton, but also induces the cellular activity of superoxide dismutase and oxidase activity. levels, but also induces structural changes in cells and tissues, and re-watering can effectively alleviate the physiological and biochemical levels of cotton under salt stress. Salt-tolerant materials have stronger salt tolerance and faster recovery after re-watering than sensitive materials.