In this study, the effects of rhizosphere aeration on leaf photosynthesis and root ion absorption in hydroponically cultivated cotton seedlings under salt stress were investigated in terms of the changes in the leaf gas exchange parameters, chlorophyll fluorescence parameters, and Na⁺ and K⁺ contents. The results showed that net photosynthetic rates decreased under salt stress and hypoxia. In the early stages of stresses, salt stress caused a more severe effect on leaf photosynthesis than oxygen deficiency. In contrast, insufficient oxygen negatively affected leaf photosynthesis in the late stages of stress than salt stress. Under mild salt stress, the additional hypoxia stress resulted in a decrease in the net photosynthetic rate, mainly due to the stomatal factor (insufficient carbon dioxide resulting from stomata closure or contraction) rather than the effect of the photosynthetic apparatus. Non-stomatal factors (injury to the photosynthetic system) gradually lowered the net photosynthetic rate with intensified salt and prolonged hypoxia stresses. The net photosynthetic rates and maximum quantum efficiency of photosystem Ⅱ in cotton leaves under rhizosphere aeration were significantly higher than those in cotton leaves without rhizosphere aeration under the same salt stress. It was suggested that oxygen deficiency in the root environment worsened the adverse effect of salt stress on photosynthesis. Ion accumulation in different organs of cotton seedlings indicated that salt stress reduced the capability of K⁺ absorption, Na⁺ exclusion, and the selective transportation of K⁺, thus decreasing K⁺ content and increasing Na⁺ content and the [Na⁺]/[K⁺] ratio both in roots and leaves. However, rhizosphere aeration could significantly improve the above conditions induced by salt stress, and reduce the[Na⁺]/[K⁺] ratio. Moreover, K⁺ and Na⁺ contents in roots were more influenced by salt stress, whereas K⁺ and Na⁺ contents in leaves were more affected by rhizosphere aeration. In conclusion, salt stress and oxygen deficiency around roots can lead to the decline in the net photosynthetic rate, injury of photosynthetic apparatus, and a disorder in the ion balance in cotton seedlings. On the other hand, rhizosphere aeration could alleviate the adverse effects of salt stresses on photosynthesis, increase the selective absorption and accumulation of K⁺ in roots and leaves, thereby reducing the ratio of [Na⁺]/[K⁺], and improving the adaptability and resistance of cotton seedling to salt stress.