Nutrient deficiency is a vital limiting factor for crop yield and quality improvement. It has restricted the yield and quality of natural rubber for a long time because of the depletion of soil potassium (K) and magnesium (Mg) and their low plant availability in the Laterite soil of rubber plantations, South China. Rubber seedlings of “CATAS 7-33-97” was chosen as test material, the material composition characteristics of rubber leaves under K and Mg deficiency were studied by Fourier transform infrared spectroscopy (FTIR). The changes and differences of FTIR characteristic peaks of leaves were analyzed, and the material compositions and structures were discussed. It would provide some physiological evidence of rubber plants subjected to K and Mg deficiency stress. The results showed that: (1) the characteristic peaks of 1 554, 1 519 and 1 075 cm^-1 disappeared due to K deficiency, implying that the structure of amide Ⅱ band, phenolic compounds and carbohydrate were broken. The relative absorbance of all characteristic peaks was increased compared with normal treatments, suggesting that protein and carbohydrate were accumulated in leaf to reduce their translocation efficiency. (2) The absorption peak at 1 554 cm^-1 shifted 6 cm^-1 to high frequency as 1 560 cm^-1 when the plant was subject to Mg deficiency, which indicated that the structure of the protein amide Ⅱ band was changed. Meanwhile, Mg deficiency decreased the relative absorbance in the range of 1 550~1 350 cm^-1, implying that Mg deficiency decreased the contents of polysaccharides and lipid compounds of the leaf cell wall. The three absorption peaks in the wave number of 1 550~1 350 cm^-1 were more sensitive to Mg deficiency than other absorption peaks, indicating that the wave band could better represent the magnesium nutrition status of rubber plant leaves. (3) The relative absorbance and intensity of each absorption peak decreased obviously at both K and Mg deficiency. Absorption peaks at 1 554, 1 519 and 1 075 cm^-1 disappeared similar to that K deficiency, which indicated that the chemical structure of protein amide Ⅱ band, phenols and carbohydrates was destroyed. Meanwhile, the absorption peak of 1 057 cm^-1 shifted to the high frequency direction by 11 cm^-1 to 1 068 cm^-1, implying the molecular structure of pectin polysaccharides changed in rubber leaves. In conclusion, K deficiency caused a large accumulation of protein and carbohydrates in rubber leaves, and magnesium deficiency caused the decrease of polysaccharide and lipid compounds in the leaf cell wall. However, the contents of protein, lipid and carbohydrates decreased significantly when the plant was subjected to both K and Mg deficiency. The results showed that FTIR technology was feasible for qualitative analysis of the material components of rubber leaves under nutrient deficiency and could provide new ideas and methods for studying the mechanism of K and Mg nutrition and physiological metabolism of the rubber trees.