Abstract: There are many types of saline-alkali land in Xinjiang, and salt accumulation is a serious problem. Therefore, this study aimed to explore the effects of different saline-alkali stresses on the absorption, transportation, and metabolism of cotton nutrients and to reveal the tolerance mechanism of cotton to different salt and alkali stresses to provide a theoretical basis for cotton cultivation on different types of saline-alkali land in Xinjiang. Four treatments were used in this study: control (CK), NaCl stress (CS), Na₂SO₄ stress (SS), and alkali (NaHCO₃+Na₂CO₃) stress (AS). The effects of different salt and alkali stresses on the content and metabolism of nutrient elements in cotton roots and leaves were explored using ionomics and metabonomics. Compared with CK, the total biomass of CS, SS, and AS treatments decreased significantly (P<0.05) by 51.7%, 47.8%, and 52.3%, respectively. Compared with CK, CS treatment significantly (P<0.05) increased the content of N in leaves and the content of P in roots; significantly (P<0.05) decreased the contents of P, K, Ca, Mg, and S in leaves; the contents of N, P, K, Ca, Mg, and S in stems; the content of N, Ca, and Mg in roots. Under AS treatment, the contents of P, K, Ca, Mg and S in leaves; the contents of N, P, Ca, Mg and S in stems; and the contents of N, P and S in roots significantly (P<0.05) decreased, while Mg content in roots significantly (P<0.05) increased over the CK treatment. Seven differential metabolic pathways were screened from cotton leaves and roots under the CS treatment; 16 and 29 differential metabolic pathways were screened from cotton leaves and roots under the SS treatment; and eight and 18 differential metabolic pathways were screened from cotton leaves and roots under the AS treatment. NaCl stress inhibited the transport of P, Ca, Mg, S, and N uptake in cotton but promoted the transport of N and K; NaCl stress had relatively little effect on metabolism, only the accumulation of amino acids and organic acids. Na₂SO₄ stress did not significantly inhibit the absorption and transport of N and K but promoted the absorption of Mg and S. However, it inhibited the absorption and transport of Ca and Mg in cotton. Na₂SO₄ stress had a significant impact on metabolism. The significant accumulation of S incotton promotes the metabolism of amino acids, and the enhancement of amino acid metabolism also indirectly promotes the intensity of other metabolic pathways, making cotton more tolerant to Na₂SO₄. Alkali (NaHCO₃+Na₂CO₃) stress inhibited N and S uptake and P, K, Ca, Mg, and S transport but increased Mg uptake, which significantly changed the metabolism of organic acids in cotton, enhanced the metabolism of organic acids in roots, significantly accumulated organic acids, and significantly accumulated linoleic acid in leaves.