Salt dust in rump lake areas in arid regions has long been considered an extreme stressor for both native plants and crops. In recent years, research on the harmful effects of salt dust on native plants has been published by many scholars, but the effect on crops has been little studied. In this work, in order to determine the impact of salt dust storms on cotton, we simulated salt dust exposure of cotton leaves in Ebinur Basin in Northwest China, and measured the particle sizes and salt ions in the dust, and the photosynthesis, the structure and the cell physiological properties of the cotton leaves. (1) Analysis found that the salt ions and particle sizes in the salt dust used in the experiments were consistent with the natural salt dust and modeled the salt dust deposition on cotton leaves in this region. (2) The main salt cations on the surface and inside the cotton leaves were Na+, Ca2+, Cl- and SO4 2-, while the amounts of CO3 - and HCO3 - were low. From the analysis, we can order the quantity of the salt cations and anions ions present on the surface and inside the cotton leaves as Na+>Ca2+>Mg2+>K+ and Cl->SO4 2->HCO3 ->CO3 -, respectively. Furthermore, the five salt dust treatment groups in terms of the total salt ions on both the surface and inside the cotton leaves were A(500g.m-2)>B(400g.m-2)>C(300g.m-2)>D(200g.m-2)>E(100g.m-2)>F(0g.m-2). (3)The salt dust that landed on the surface of the cotton leaves can significantly influence the photosynthetic traits of Pn, PE, Ci, Ti, Gs, Tr, WUE, Ls, φ, Amax, k and Rady of the cotton leaves. (4)Salt dust can significantly damage the physiological functions of the cotton leaves, resulting in a decrease in leaf chlorophyll and carotenoid content, and increasing cytoplasmic membrane permeability and malondialdehyde (MDA) content by increasing the soluble sugar and proline to adjust for the loss of the cell cytosol. This increases the activity of antioxidant enzymes to eliminate harmful materials, such as the intracellular reactive oxygen and MDA, thus reducing the damage caused by the salt dust and maintaining normal physiological functioning. Overall, this work found that the salt dust deposition was a problem for the crop and the salt dust could significantly influence the physiological and biochemical processes of the cotton leaves. This will eventually damage the leaves and reduce the cotton production, leading to agricultural economic loss. Therefore, attention should be paid to salt dust storms in the Ebinur Basin and efficient measures should be undertaken to protect the environment.