The common peak ratio and variant peak ratio were calculated by FTIR spectroscopy of six medicinal plants of polygonatum. The index sequence of common peak ratio and variant peak ratio of six medicinal plants was established and the FTIR spectroscopy was analyzed by cluster analysis, which indicated the sibship of the six medicinal plants. polygonati rhizoma, polygonati odorati rhizoma and their adulterant such as Polygonatum filipes Merr., Polygonatum macropodium Turcz. and Polygonatum humile Fisch Ex Maxim. could be identified by comparing second derivative spectrum of the samples. FTIR with good characteristics such as simple and rapid procedures, nondestructive testing, small amount of sample required, good reproducibility and specificity of fingerprint, provides a new method for identification of polygonati rhizoma, polygonati odorati rhizoma and their adulterant.