The application of traditional Chinese medicine (TCM) and their preparations have a long history. With the deepening of the research, the market demand is increasing. However, wild resources are so limited that it can not meet the needs of the market. The development of wild and cultivated samples and research on accumulation dynamics of chemical component are of great significance. In order to compare composition difference of different parts (root, stem, and leaf) of wild and cultivated G. rigescens, Fourier infrared spectroscopy (FTIR) and second derivative spectra were used to analyze and evaluate. The second derivative spectra of 60 samples and the rate of affinity (the match values) were measured automatically using the appropriate software (Omnic 8.0). The results showed that the various parts of wild and cultivated G. rigescens. were high similar the peaks at 1 732, 1 643, 1 613, 1 510, 1 417, 1 366, 1 322, 1 070 cm-1 were the characteristic peak of esters, terpenoids and saccharides, respectively. Moreover, the shape and peak intensity were more distinct in the second derivative spectrum of samples. In the second derivative spectrum range of 1 800~600 cm-1, the fingerprint characteristic peak of samples and gentiopicroside standards were 1 679, 1 613, 1 466, 1 272, 1 204, 1 103, 1 074, 985, 935 cm-1. The characteristic peak intensity of gentiopicroside of roots of wild and cultivated samples at 1 613 cm-1(C—C) was higher than stems and leaves which indicated the higher content of gentiopicroside in root than in stem and leaves. Stems of wild samples at 1 521, 1 462 and 1 452 cm-1 are the skeletal vibration peak of benzene ring of lignin, and the stem of cultivated sample have stronger peak than other samples which showed that rich lignin in stems. The iInfrared spectrum of samples were similar with the average spectral of root of wild samples, and significant difference was found for the correlation between second derivative spectrum of samples and average spectral of wild samples root, and the sequence of similarity was root>stem>leaf. Therefore, FTIR combined with second derivative spectra was an express and comprehensive approach to analyze and evaluate in the imperceptible differences among different parts of wild and cultivated of G. rigescens.