Potassium (K) and boron (B) are essential nutrient elements for plants, and the elements play an important role for plant growth, development and physiological metabolism. Cotton has a higher demand for K and B; K deficiency or B deficiency often occurs in cotton though. To reveal the component changes in functional leaf of cotton under K and B stress and investigate effects on material composition from K and B. A pot experiment was conducted at Huazhong Agricultural University. (1) the characteristic peaks at 1 546.86,1 438.85, 1 153.39 and 1 024.17 cm-1 disappeared due to B deficiency, and relative absorbance of other characteristic peaks was decreased compared with normal, which suggested that the structures of protein, fiber, soluble sugar and ribosome in cotton functional leaf changed and decreased in cotent when lack of K. (2) the relative absorbance of all characteristic peaks was increased in the B-deficient cotton leaves compared with normal, suggesting B deficiency leads to the accumulation in leaves of protein, and fiber, soluble sugar and other carbohydrates because of the hindered transportation. (3) lack of both potassium and boron, induced significant changes to both the locations and relative absorbance of characteristic peaks, and the content of protein, and soluble sugar and other carbohydrates increased , while the content of nucleic acids and polysaccharides dropped. K deficiency led to the structures of protein, fiber, soluble sugar and ribosome in cotton functional leaf changed and decreased in content ; B deficiency gave rise to the accumulation in leaves of protein, and fiber, soluble sugar and other carbohydrates; the content of protein and soluble sugar and other carbohydrates increased, while the content of nucleic acids and polysaccharides dropped when K and B were all in short supply .