Objective:To compare and analyze rhizome and main root of Ginseng Radix et Rhizoma (GRR); To provide the basis of whether removing the rhizome of Ginseng (RG) when processing by checking whole consistency of chromatographic fingerprints from rhizome and main root of GRR.Methods:The chromatographic consistency of different parts of GRR samples was compared using high performance thin layer chromatography (HPTLC); HPLC was used to determine the fingerprint of different parts of GRR, and combining it with the reference substance for common peak identification and similarity analysis; differences were analyzed using principal component analysis and orthogonal partial least squares discriminant analysis (OPLS-DA).Results:In the HPTLC spectrum, the characteristic spectra of rhizome and main root of GRR and whole GRR were similar, and there was a clear total of 7-9 spots. HPLC fingerprints of RRR presented 13 common peaks, and identified 6 peaks, including ginsenoside Rg1&Re (mixed), Rf, Rb1, Rc, Ro and Rd; the similarity of all samples ranged from 0.842 to 0.993; the differences in peak areas comprehensively contributed to the similarity differences between samples, with head being the main influence; ginsenoside Ro, Rb1 and other six components were differential markers, and the relative content in the head of GRR is significantly higher than that in the main root. Conlusions 　The analysis of differential profiling of chemical constituents showed that the chemical substances are almost the same between the head and the main root. The processing of GRR to remove head will result in the loss of ginsenosides, the overall effective component of GRR. Considering the human and resource costs, it was suggested that the whole root of GRR, instead of removing its rhizome, could be used in classical and traditional prescriptions.