Five herbs named as Chinese Danggui (CDG), Japanese Danggui (JDG), Korea Danggui (KDG), Lovage root (LR) and Angelica root (AR) are widely and confusedly used in eastern and western countries owing to their homonym. These herbs come from different plant species resulting in the variety of bioactive components and medical efficacy. A method combing tri-step IR macro-fingerprinting techniques with statistical pattern recognition was therefore employed discriminate the five herbs in order to assure their genuineness. A total of 26 samples were collected and identified by conventional Fourier transform infrared (FTIR) spectroscopy, second derivative infrared (SD–IR) spectroscopy and two-dimensional correlation infrared (2D-COS IR) spectroscopy. CDG and KDG were easily differentiated from others herbs by FTIR and SD–IR spectra. The characteristic peaks of CDG were located at 1068, 1051, 990, 909 and 867cm−1, whilst KDG contained the peaks located at 1628, 1565, 1392, 1232 and 1136cm−1. By 2D-COS IR spectra, the bands in the range of 950–1110cm−1 could be a characteristic range to identify the five herbs. There were six auto-peaks located at 978, 991, 1028 (strongest), 1061, 1071 and 1097cm−1 for CDG, six auto-peaks at 975, 991, 1026, 1053, 1070 (strongest) and 1096cm−1 for KDG, five auto-peaks at 970, 1009, 1037, 1070 and 1096 (strongest) cm−1 for JDG, five auto-peaks at 973 (strongest), 1009, 1033, 1072 and 1099cm−1 for LR, and five auto-peaks at 974 (strongest), 1010, 1033, 1072 and 1099cm−1 for AR. Classification analysis of FTIR showed that these species located in different clusters. The results indicate the tri-step infrared macro-fingerprinting combines with principle component analysis (PCA) is suitable to rapidly and nondestructively differentiate these herbs.