Potassium (K) deficiency affects cotton growth. The substitution effects of sodium (Na) and potassium research have been the focus of attention at home and abroad. The aim of this paper was to study the substitution effects of Na and K on material composition in leaf of two kinds of K-efficiency cotton genotypes (HG103 and LG122) using Fourier to transform infrared (FTIR) spectroscopy. The results showed that: (1) the increment of the relative absorbance of HG103 at peaks 2　960, 2　855 and 2　926 cm-1 were the same with LG122 with addition of Na in deficient K, while at peaks 1　078 and 1　103 cm-1, the increment of HG103 was higher than LG122, indicating that in deficient K, Na could promote the synthesis of carbohydrate, protein and esters, wherein the promoting effect on carbohydrate of HG103 was greater than LG122, while for protein and esters, there has no difference. However, the decrement of the relative absorbance at these five peaks of HG103 was higher than LG122 with addition of Na in adequate K, suggesting that in adequate K, the inhibitory effect of Na on carbohydrate, protein and esters of HG103 was less LG122. (2) the peaks at 1　734 and 1　437 cm-1 disappeared due to K dificiency, when added Na, these peaks did not appear, implying that the structure of amideⅠband and cellulose was broken when lack of K when added Na has no changes.