In the present paper, Fourier transform infrared spectroscopy (FTIR) combined with two-dimensional correlation spectroscopy (2D-IR) was used for the identification of Cistanche deserticola from its adulterants, Boschniakla rossica and Cynomorium songaricum. The results showed that these IR spectra showed their different macro-fingerprint feathers: the charactersistic peaks for Cistanche deserticola were located at ～1 730 and 931 cm-1. While absorption peaks at ～1 510, 1 375 and 1 266 cm-1 were only found in Boschniakla rossica. And the strongest peak of Cynomorium songaricum was at 1 614 cm-1. Differences were more obvious in the second derivative IR spectra: the intensities of the four peaks of Cistanche deserticola at ～1 453, 1 336, 931, and 892 cm-1 were strong, among which the peak at ～931 cm-1 was sharp and the strongest in intensity. There was the strongest peak at ～1 509 cm-1 for Boschniakla rossica. In addition, the shape of peaks at ～1 633 and 1 161 cm-1 was wider and the intensities were stronger. While the shape of peak at ～1 682 cm-1 was sharp, and also the intensity of peak at 1 605 cm-1 was stronger. According to the features of the IR spectra of each kind, a quick and accurate method based on FTIR for the identification of Cistanche deserticola was established.