Saline-alkali stress has always been a key factor restricting crop production in Xinjiang. Sea Island cotton is one of the main cash crops in Xinjiang and an important textile raw material. This experiment is based on the main Island cotton varieties Xinhai 31 (XH31), Xinhai 35 (XH35), Xinhai 43 (XH43) and Xinhai 48 (XH48), in the Aksu area of Xinjiang, involving treatment with neutral salt mixed with NaCl and Na₂SO₄ at 1:1 mole ratio and treatment with alkali salt mixed with NaCl and NaHCO₃ at 1:1 mole ratio. The objective was to explore the response of biomass allocation and root growth in Sea Island cotton seedlings to mixed saline-alkali stress. Total salt concentrations (Na⁺) in the different treatments were 0(CK), 120, 180, 240, 300, and 360 mmol/L. The differences in root morphological characteristics of Sea Island cotton seedlings under the two salt stress conditions, including biomass, root length, root volume, and root surface area, and root system morphological characteristics at different stem levels, were analyzed. Under the condition of neutral salt, the total root length, total surface area, total volume, and total root tip number of Sea Island cotton seedlings increased significantly or decreased slightly at salt concentrations of 0-180 mmol/L, and the fine root length of Sea Island cotton seedlings increased significantly, especially at a concentration of 120 mmol/L. When the concentration was higher than 180 mmol/L, the root parameters decreased significantly with the increase in salt concentration. Under the condition of alkaline salts, the total number of root tips and fine and middle root tips of Xinhai 31 were higher than that of CK at 120 mmol/L salt concentration, and the other parameters decreased with the increase in salt concentration. The biomass and root-shoot ratio decreased gradually with the increase in salt concentration under the two salt treatments, and the degree of reduction increased from low to high. Low salt (120 mmol/L) environment can promote the elongation of fine roots, so that Sea Island cotton seedlings can absorb more nutrients and water, which is the response of roots when exposed to a low salt environment. High salt environment causes greater damage to Sea Island cotton seedlings.