Semen Glycines Nigrae and Semen Pharbitidis containing a large amount of fats and proteins are commonly used in Chinese herbal medicine. Tri-step infrared spectroscopy was applied to fast analyze and identify the two samples. In the conventional infrared spectroscopy, the samples both have obvious characteristic absorption peaks at 1 745 cm-1 assigned to the stretching mode of CO in esters. Furthermore, the two kinds of herbs have the peaks at 1 656 and 1 547 cm-1 assigned to the amide Ⅰ and Ⅱ bands of protein. Obviously, the infrared spectra of herbs demonstrate that protein and fat is the major component in two kinds of herbs, and the relative intensity of the peaks assigned to fat and protein indicate their relative content is different. And the result is consistent with the reported. In the second derivative spectra, Semen Pharbitidis has a peak at 1 712 cm-1 assigned to the organic acid, however, Semen Glycines Nigrae has not this absorption peak. In addition, in the second derivative spectra, appeared more differences between the two samples in shape and intensity of the peaks. In two-dimensional correlation infrared spectra, the two samples were visually distinguished due to their significant differences in auto-peak position and intensity. In the region of 1 500~1 700 cm-1, Semen Glycines Nigrae has two autopeaks and Semen Pharbitidis has three autopeaks. In the region of 2 800~3 000 cm-1, the samples both have two autopeaks, but the position of the strongest autopeak is different. It was demonstrated that the Tri-step infrared spectroscopy were successfully applied to fast analyze and identify the two kinds of samples containing the same major component, and made sure the foundation for future researches.