Boron (B) is an essential trace element for higher plants, the threshold between deficiency and toxicity is narrow, so the problems of yield and quality of crops due to B deficiency and B toxicity have been attracting great attention home and abroad. To investigate the effects on the component and structure changes in leaf of two kinds of citrus rootstocks (citrange and trifoliate orange) under B stress situations by using Fourier transform infrared (FTIR) spectroscopy. The results showed that: (1) the growth of citrus rootstock was inhibited by the low B and high B stress situations. Symptoms of B-toxicity were first appeared in old leaves as tip yellowing in trifoliate orange, in contrast, almost no visible symptoms occurred in citrange, suggesting that citrange was more tolerant to B-toxicity than trifoliate orange. (2) the characteristic peaks were at 1 153, 1 053 and 1 028 cm-1 disappeared due to low B stress in trifoliate orange, but only 1 055 cm-1 disappeared in citrange, and relative absorbance of other peaks was increased compared with control, suggesting that the structure of cellulose glycosides, soluble sugar and ribosome in leaf changed and other components increased under low B stress in trifoliate orange, only soluble sugar changed in citrange ones. Thus, the effect of low B stress on trifoliate orange is higher than that of citrange. (3) the characteristic peaks at 1 153, 1 053 cm-1 disappeared due to high B stress in trifoliate orange, however, 1 024 cm-1 disappeared in citrange, the relative absorbance of other peaks was reduced compared with control, indicated that the structure of protein and soluble sugar in leaf changed and other compositions reduced under high B stress in trifoliate orange, and ribosome changed in citrange ones. Therefore, the effect of high B stress on trifoliate orange is higher than that of citrange in polysaccharide structure. Results show that citrange was more tolerant to low B and high B stress than trifoliate orange, and one of the key factors contributing to the result is the differences of B effect on chemical composition and structure between two rootstocks.